Intelliseal — Microsoft 365 Tenant Security & Deployment Checklist

Consolidated, step-by-step guide merging five source documents. Duplicate/overlapping steps have been merged into a single authoritative entry; where two documents configure the same underlying control through different named policies, the item is flagged with a ๐Ÿ”€ Conflict check note instead of being silently merged, since those need verifying in Intune rather than assumed identical.

Sources: Microsoft 365 Baseline Security Policy · SOP for Setting up Microsoft 365 using Business Premium · Intelliseal Defender for Business Baseline SOP v1.0 · Microsoft Intune Basic Setup (Windows) · Microsoft 365 Business Premium Setup Package Compiled: 14 Aug 2026
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How to use this: Pick your name from the dropdown in the top bar, then click ๐Ÿ– Claim on a step before you start it so your colleague sees it's taken — ticking the checkbox marks it done and releases the claim. Status is shared live with everyone who has this page open. Click Guide on any item to see the exact portal path and steps. Items marked merged combine overlapping instructions from more than one source document.
๐Ÿ”€ Conflict-check protocol: the Intune Basic Setup guide and the Defender for Business Baseline SOP each configure a couple of the same underlying controls (Antivirus, SmartScreen) as separately named policies. Items below carrying a purple Conflict check note tell you exactly what to compare. Before assigning either policy tenant-wide: open Intune admin center → Devices → a test device → Device configuration / Antivirus, and check the status column for Conflict. If one shows up, keep only the more complete policy, remove or disable the duplicate, and go back to the Microsoft 365 Baseline Security Policy document and set that control's status to "Not yet configured" until you've consolidated it into one profile.

Executive summary — Quick Engineer Checklist

  1. Add & verify domain, configure mail flow (MX/SPF/DKIM/DMARC)
  2. Set up least-privilege admin roles; enable Security Defaults or baseline Conditional Access (MFA + block legacy auth)
  3. Enable SSPR and review Secure Score
  4. Turn on Defender for Office 365 preset security policies (Standard); create shared mailboxes
  5. Disable external auto-forwarding; enable mailbox auditing
  6. Create the Intune device group, then enrol devices, and build compliance, BitLocker, config, and LAPS profiles
  7. Connect Intune with Defender, onboard devices, configure AV/ASR/EDR/web protection baselines
  8. ๐Ÿ”€ Check Intune for policy conflicts (Antivirus, SmartScreen) between the Defender baseline and Intune Basic Setup profiles before assigning tenant-wide
  9. Configure SharePoint sites, external sharing, and OneDrive storage/sync restrictions
  10. Configure DLP, sensitivity labels, retention, audit log, eDiscovery & litigation hold
  11. Enable OneDrive Known Folder Backup + litigation hold on key mailboxes
  12. Set up Teams/Outlook collaboration policies
  13. Onboard users, assign licenses, deliver training
  14. Schedule third-party backup and confirm completion criteria

1. Initial Tenant & Domain Setup

Source: Setup SOP (Step 1–2) · Baseline Policy (4.6)

Add and verify your custom domain
Setup SOP
admin.cloud.microsoft → Settings → Domains → Add domain
  1. Sign in to the Microsoft 365 admin center.
  2. Go to Settings > Domains > Add domain.
  3. Enter the custom domain name and follow the wizard to add the required DNS verification (TXT) record at your domain registrar.
  4. Confirm verification completes in the admin center before continuing.
๐Ÿ’ก DNS TXT verification usually completes within minutes but can take up to 72 hours to propagate fully — if verification fails immediately after adding the record, wait and retry rather than re-generating a new value. Keep the original *.onmicrosoft.com domain intact as a permanent fallback; never delete it even after your custom domain is set as default.
Configure mail flow: MX, SPF, DKIM, DMARC
mergedSetup SOPBaseline Policy 4.6

MX record — use the exact value provided by the Microsoft 365 domain setup wizard to route mail to Exchange Online.

SPF (Sender Policy Framework)

  • Add a DNS TXT record: v=spf1 include:spf.protection.outlook.com -all

DKIM (DomainKeys Identified Mail)

  • Enable DKIM signing in the Exchange Admin Center.
  • Publish two CNAME records:
    selector1._domainkey → selector1-yourdomain-com._domainkey.<initialdomain>.onmicrosoft.com
    selector2._domainkey → selector2-yourdomain-com._domainkey.<initialdomain>.onmicrosoft.com
  • Rotate DKIM keys annually.

DMARC (Domain-based Message Authentication, Reporting & Conformance)

  • Add a DNS TXT record: v=DMARC1; p=quarantine; rua=mailto:dmarc-reports@yourdomain.com; ruf=mailto:dmarc-forensics@yourdomain.com; pct=100; sp=quarantine; aspf=s
  • Roll out gradually: start with p=none, then move to p=quarantine, and finally p=reject.
  • Monitor DMARC aggregate/forensic reports regularly to catch spoofing attempts.
๐Ÿ’ก After publishing records, validate them with an external checker (e.g. MXToolbox) rather than trusting the admin center alone. A common mistake is ending up with two separate SPF TXT records after a migration — DNS only allows one SPF record per domain, so merge multiple include: statements into a single record.

2. Identity & Access Security

Source: Baseline Policy (4.1) · Setup SOP (Step 3) · Defender SOP (8) · M365 Business Premium Setup Package

Configure user accounts and admin roles using least privilege
Setup Package
Entra admin center → Identity → Roles & administrators
  1. Assign role-based admin permissions instead of Global Admin for day-to-day work (e.g. User Administrator, Exchange Administrator, Intune Administrator as appropriate).
  2. Limit the number of standing Global Admins to 2–4 break-glass/emergency accounts.
  3. Review role assignments periodically as part of the quarterly review (Section 10).
๐Ÿ’ก If you're licensed for Entra ID P2 (included in some Business Premium add-ons), consider Privileged Identity Management (PIM) for just-in-time admin elevation instead of standing admin role assignments — it's a stronger least-privilege control than role assignment alone.
Enable Security Defaults, or a baseline Conditional Access policy set
mergedBaseline Policy 4.1Setup SOPDefender SOP 8

Option A — Security Defaults (use if Conditional Access licensing is not available):

Entra admin center → Identity → Properties → Manage Security defaults
  • Enforces MFA for all admins and users.
  • Blocks legacy authentication (IMAP, POP3, older Office clients).

Option B — Conditional Access baseline (preferred if licensed, e.g. Business Premium):

  1. Require MFA for all admins / privileged roles.
  2. Require MFA for all users.
  3. Block legacy authentication protocols.
  4. Require MFA for risky sign-ins (requires Entra ID Identity Protection).
  5. Block sign-in from high-risk or disallowed countries.
Endpoint protection effectiveness is reduced without MFA — do not treat Defender alone as sufficient (see Defender SOP, Common Pitfalls).
๐Ÿ’ก Security Defaults and Conditional Access are mutually exclusive — Entra will prompt you to disable Security Defaults before you can enable your own CA policies. Business Premium includes Entra ID P1, which is what unlocks Conditional Access; without at least P1 you're limited to Security Defaults only.
Enable Self-Service Password Reset (SSPR)
Setup SOP
Entra admin center → Protection → Password reset
  1. Set SSPR scope to "All" or a selected group.
  2. Configure the number of authentication methods required (2 recommended).
  3. Enable registration campaign so users register methods on next sign-in.
๐Ÿ’ก Require at least two authentication methods and avoid security-questions-only registration (Microsoft has deprecated this as a standalone method). Authenticator app + phone number is the common combination for SMB tenants.
Review Secure Score monthly (target > 70%)
mergedBaseline Policy 4.5Setup SOP
security.microsoft.com → Secure Score
  1. Review outstanding recommendations and prioritise by point value / risk.
  2. Apply recommendations that don't conflict with documented exceptions.
  3. Track trend month-over-month; target score above 70%.
๐Ÿ’ก Some Secure Score recommendations are user-visible (e.g. blocking legacy auth breaks old Outlook/POP clients) — announce changes to staff beforehand to avoid a spike in helpdesk tickets right after you apply them.

3. Email & Collaboration Protection (Defender for Office 365)

Source: Setup SOP (Step 2) · Baseline Policy (4.3) · M365 Business Premium Setup Package

Enable Preset Security Policies — Standard protection
mergedSetup SOPBaseline Policy 4.3
security.microsoft.com → Email & Collaboration → Policies & Rules → Threat Policies → Preset security policies
  1. Open the Microsoft 365 Defender portal.
  2. Navigate to Email & Collaboration > Policies & Rules > Threat Policies.
  3. Click Preset security policies.
  4. Under Standard protection, click Manage Protection Settings.
  5. Assign protection to All recipients, or to specific groups/users.
  6. Click Save.
Once enabled, Standard protection automatically applies Anti-phishing, Anti-spam, Safe Links, and Safe Attachments with Microsoft-recommended settings.

Impersonation settings — within the anti-phishing policy, explicitly add your key executives/domains (e.g. CEO, CFO, finance team, your own accepted domains) as protected users/domains so impersonation protection actually triggers for targeted phishing.

๐Ÿ’ก Standard protection is the baseline; Microsoft also offers a Strict preset you can layer on top for a smaller group of high-value targets (executives, finance, HR) once Standard is validated and stable.
Disable auto-forwarding to external domains
Baseline Policy 4.3
Exchange admin center → Mail flow → Rules, or security.microsoft.com → Anti-spam → Outbound policy
  1. Set outbound anti-spam policy "Automatic forwarding rules" to Off / Automatic - System-controlled (blocks external auto-forward).
  2. Optionally create a transport rule to reject external auto-forward messages with a clear NDR message.
๐Ÿ’ก Before blocking auto-forward tenant-wide, check whether any VIP or shared mailboxes already have forwarding rules configured (Exchange admin center > Mailboxes > Mail flow settings) so you don't silently break an existing business process.
Enable mailbox auditing
Baseline Policy 4.3
Exchange admin center → Roles & admins, or Purview → Audit
  1. Confirm mailbox audit logging is enabled tenant-wide (on by default for Microsoft 365, but verify).
  2. Ensure Unified Audit Log (Section 6) is also turned on so mailbox actions are searchable.
๐Ÿ’ก Mailbox audit logging has been on by default tenant-wide since 2019, but audit log records are only retained for 180 days on Business Premium/E3 by default — if you need longer retention for investigations, that requires an audit retention policy (E5 Compliance or the add-on).
Create shared mailboxes (info@, support@, etc.)
Setup Package
admin.cloud.microsoft → Teams & groups → Shared mailboxes → Add a mailbox
  1. Create one shared mailbox per generic address needed (e.g. info@, support@, accounts@).
  2. Grant Full Access and Send As (or Send on Behalf) permissions to the relevant users.
  3. Shared mailboxes don't need a license under the storage limit (50GB) — only assign a license if it needs to exceed that, be placed on litigation hold, or use Outlook's in-place archive.
๐Ÿ’ก Shared mailboxes get 50GB free without a license. If one is likely to exceed that (busy support inbox, or needs litigation hold/in-place archive), assign it an Exchange Online license before it fills up rather than after.
Set mailbox size limits
Setup Package
Exchange admin center → Recipients → Mailboxes → select mailbox → Storage management, or a mailbox plan for bulk defaults
  1. Confirm the default mailbox plan's quota matches your licence (Business Premium includes 50GB per mailbox).
  2. Set warning/prohibit-send/prohibit-send-receive thresholds if you want tighter limits than the plan default.
Retention policies (how long mail is kept) are configured separately — see Section 6.
๐Ÿ’ก Typical defaults: a warning at ~90% of quota, prohibit-send at 100%, and prohibit-send-receive somewhat above that. Adjust thresholds if you want mailboxes to be trimmed earlier rather than relying on the plan defaults.

4. Device & Endpoint Management (Intune)

Source: Setup SOP (Step 4) · Baseline Policy (4.2) · Intune Basic Setup (Windows) · M365 Business Premium Setup Package

Enable Automatic Device Enrollment into Intune
mergedSetup SOPIntune Basic Setup
Intune admin center → Devices → Enrollment → Windows → Automatic Enrollment
SettingValue
MDM user scopeAll
WIP user scopeNone

Result: when a user signs into a company Windows PC with their Microsoft 365 account, the device auto-enrols into Intune.

The M365 Business Premium Setup Package also references enrolling macOS and mobile devices. The detailed steps in the other four documents only cover Windows 10/11 — if you manage macOS/mobile in this tenant, treat this whole section as a Windows-only baseline and build equivalent macOS/iOS/Android policies separately.
๐Ÿ’ก Enrollment typically completes within a few minutes of first sign-in but can take longer on a slow connection. On Windows this happens via Settings > Accounts > Access work or school — users don't need to install anything manually if automatic enrollment is on.
Create the Intune device group for Windows devices
Intune Basic Setup
Entra admin center → Entra ID → Groups → New Group
SettingValue
Group typeSecurity
Group nameIntune-Windows-Devices
Entra roles can be assigned to groupNo
Membership typeAssigned
  1. Add your pilot/test Windows devices to this group first.
  2. Use this single group as the assignment target for every Intune policy in this section and in Section 5 (compliance, BitLocker, Defender AV, ASR, EDR, LAPS, update rings).
  3. Recommended: stay on an Assigned group with manually added devices until you're comfortable, then switch to a dynamic device group.
๐Ÿ”€ Naming consistency check: your working notes separately flagged an EDR group called "MDATP" that should include all devices. Confirm whether "MDATP" and "Intune-Windows-Devices" are meant to be the same group. If they're different, standardise on ONE group for all Defender/Intune policy assignments so nothing is scoped to a partial device list.
๐Ÿ’ก Consider a naming convention for security-related groups (e.g. a consistent prefix) so it's obvious at a glance which groups feed into policy assignments, especially once you have several overlapping device/user groups.
Create device compliance policies
mergedSetup SOPBaseline Policy 4.2Intune Basic Setup
Intune admin center → Devices → Compliance → Create policy

Platform: Windows 10 and later · Profile: Windows 10/11 compliance policy · Name: Win-Compliance-Basic

SettingRequired value
Device Health > BitLockerRequire
System Security > Device Security > FirewallRequire
System Security > Device Security > AntivirusRequire

Assign to: Intune-Windows-Devices

  • Mobile: require Outlook Mobile with app protection (block native mail apps if needed); block jailbroken/rooted devices.
  • Optional stretch goal: mark non-compliant if the Defender for Endpoint machine risk score exceeds your threshold (needs the Defender connector from item below).
This policy only checks/reports BitLocker status — it doesn't turn encryption on. Pair it with the BitLocker Disk Encryption policy below so devices aren't flagged non-compliant before encryption is actually enforced.
๐Ÿ’ก The compliance policy alone doesn't block anything — it just marks a device compliant or not. To actually restrict access for non-compliant devices you need a Conditional Access policy that requires "Device marked as compliant" (Section 2). Also set a noncompliance actions schedule (e.g. email the user immediately, mark noncompliant after 1 day) so people get a warning before being blocked.
Create BitLocker Disk Encryption policy
Intune Basic Setup
Intune admin center → Endpoint security → Disk encryption → Create Policy

Platform: Windows · Profile: BitLocker · Name: Win-BitLocker

SettingValue
Require Device EncryptionEnabled
Configure Recovery Password RotationRefresh on, for both Entra ID-joined and hybrid-joined devices
Choose drive encryption method and cipher strengthEnabled
Encryption method — fixed data drivesXTS-AES 128-bit (default)
Encryption method — operating system drivesXTS-AES 128-bit (default)
Encryption method — removable data drivesAES-CBC 128-bit (default)

Assign to: Intune-Windows-Devices

This is the policy that actually enables encryption; the compliance policy above only reports on it. Deploy this one first (or together), so devices don't get marked non-compliant before encryption has had a chance to finish.
๐Ÿ’ก Recovery keys are automatically escrowed to Entra ID once this policy is applied. Make sure your helpdesk process for retrieving a key (Entra admin center > Devices > select device > BitLocker keys) is documented, since a locked-out user will need this quickly.
Create configuration profiles (Wi-Fi/Email, browser & app control, screen lock, SmartScreen)
mergedSetup SOPIntune Basic Setup
Intune admin center → Devices → Configuration → Create → New Policy

Platform: Windows 10 and later · Profile type: Settings catalog · Name: Win-Basic-Settings

Setting (search term)Value
Require a password when a computer wakes (on battery)Enabled
Require a password when a computer wakes (plugged in)Enabled
Interactive Logon Machine Inactivity Limit900 (seconds — 15 min screen lock)
Configure Microsoft Defender SmartScreenEnabled
Prevent bypassing SmartScreen prompts for sites (device & user)Enabled
Prevent bypassing SmartScreen download warnings (device & user)Enabled

Assign to: Intune-Windows-Devices

  • Also add Wi-Fi and Email auto-configuration profiles for managed devices.
  • Add browser and app control settings as needed (e.g. blocked app lists).
๐Ÿ”€ Conflict check — SmartScreen: the Defender for Business baseline (Section 5) also sets SmartScreen/Network protection through its own Web & Ransomware Protection policy. Having two separate policies configure SmartScreen can show as a Conflict on the device in Intune. Check Devices > a test device > Device configuration for a conflict status; if one appears, keep the setting in only one policy (recommend keeping it here, since this profile also covers the rest of the workstation baseline), remove it from the other, and mark the removed control "Not yet configured" in the Microsoft 365 Baseline Security Policy document until it's consolidated.
๐Ÿ’ก 900 seconds equals a 15-minute screen lock — adjust to match any compliance framework you're bound by (e.g. many standards call for 15 minutes or less). Test the Settings Catalog profile on one pilot device before wide assignment, since setting catalog conflicts can be harder to diagnose than classic profile conflicts.
Create and assign Intune Security Baseline policies
Intune admin center → Endpoint security → Security baselines → Create profile
  1. Choose the relevant baseline (e.g. "Security Baseline for Windows 10/11", "Microsoft Defender for Endpoint Security Baseline").
  2. Review pre-configured settings against your organisation's needs and adjust exceptions.
  3. Assign to a pilot group first, validate, then expand to all devices.
Not detailed in the current SOPs — recommended addition since your tracker lists "Security Baseline Policies: Not yet created". Document the finalised settings back into the Baseline Security Policy once created.
๐Ÿ’ก Intune security baselines are versioned (e.g. a dated "Security Baseline for Windows 10/11" release) — always pick the current version and skim its change notes, since Microsoft periodically tightens or retires individual settings between versions.
Deploy apps via Intune / Company Portal
Setup SOP
Intune admin center → Apps → All apps → Add
  • Deploy Microsoft 365 Office apps (via Intune, or directly from the M365 portal for user-installed).
  • Publish self-service apps through Company Portal.
๐Ÿ’ก Choose an update channel when deploying: Current Channel gets new features fastest, Monthly Enterprise Channel gets one bundled update a month and is the steadier choice for most business fleets.
Enable remote lock / wipe / locate and configure Windows Update rings (patch management)
mergedSetup SOP
Intune admin center → Devices → Windows → Update rings for Windows 10 and later
  1. Confirm remote lock, wipe and locate actions are available for enrolled devices (Devices > All devices > select device).
  2. Create Update rings: define deferral periods for feature/quality updates, active hours, and whether users can pause updates.
  3. Assign rings in phases: pilot ring first, then broad rings.
๐Ÿ’ก A 0-day deferral on the pilot ring means untested patches hit those devices the same day Microsoft ships them — consider a short deferral (3–7 days) even for pilot, and a longer one (2–3 weeks) for the broad ring, so problem patches get caught before they reach most of the fleet.
Enforce Intune App Protection Policies (MAM) for mobile access
Baseline Policy 4.2
Intune admin center → Apps → App protection policies → Create policy
  1. Target iOS/Android platforms.
  2. Require PIN, restrict copy/paste and save-as to unmanaged apps, require encryption of app data.
๐Ÿ’ก App protection (MAM) policies are the main control for BYOD phones that you don't want fully enrolled in MDM — they protect corporate data inside apps like Outlook without requiring the user to hand over full device management.
Deploy Windows LAPS (Local Administrator Password Solution)
Intune Basic Setup

Step 1 — turn on LAPS for the tenant

Entra admin center → Devices → Device settings
SettingValue
Enable Microsoft Entra Local Administrator Password Solution (LAPS)Yes

Step 2 — create the Intune LAPS policy

Intune admin center → Endpoint security → Account protection → Create Policy

Platform: Windows · Profile: Local admin password solution (Windows LAPS) · Name: Win-LAPS

SettingValue
Backup DirectoryBackup the password to Microsoft Entra ID only
Password Age (Days)7
Password ComplexityLarge letters + small letters + numbers + special characters
Password Length16
Post Authentication ActionsReset the password and logoff the managed account
Post Authentication Reset Delay8
Automatic Account Management — EnabledThe target account will be automatically managed
Automatic Account Management — TargetManage a new custom administrator account
Automatic Account Management — Randomize NameNo random numeric suffix
Automatic Account Management — Enable AccountEnabled
Automatic Account Management — Name/PrefixLAPSAdmin

Assign to: Intune-Windows-Devices

๐Ÿ’ก After assigning the policy, verify retrieval actually works before relying on it: Entra admin center > Devices > select a test device > Local administrator password. Confirm whoever handles lockouts (helpdesk) knows this is where to look.
Connect Intune with Microsoft Defender for Endpoint
Intune Basic Setup
Intune admin center → Endpoint security → Microsoft Defender for Endpoint
SettingValue
Allow Microsoft Defender for Endpoint to enforce Endpoint Security ConfigurationsOn
This is the connector that lets Intune and Defender share device risk/compliance signals. Turn this on before doing the onboarding and EDR steps in Section 5 — it's a prerequisite, not optional.
๐Ÿ’ก Allow up to 24 hours after turning this on for the connector to fully sync between Intune and Defender — if a device doesn't show up where expected right away, that's usually just propagation delay rather than a misconfiguration.
Create the Intune EDR configuration profile (Win-EDR)
Intune Basic Setup
Intune admin center → Endpoint security → Endpoint detection and response → Create Policy

Platform: Windows 10 and later · Profile: Endpoint detection and response · Name: Win-EDR

SettingValue
Microsoft Defender for Endpoint client configuration package typeAuto from connector
Sample SharingAll (Default)

Assign to: Intune-Windows-Devices

๐Ÿ”€ Not the same as onboarding: this EDR configuration profile is separate from the "Onboarding" policy in Section 5 (that one pushes the sensor; this one sets EDR mode/telemetry). You need both. Double-check both are assigned to the same device group — see the naming-consistency note under "Create the Intune device group" above.
๐Ÿ’ก "Sample Sharing = All" sends file samples to Microsoft for analysis; if you have data-residency or confidentiality concerns, use "Send safe samples automatically" instead, which limits what's shared.

5. Endpoint Threat Protection (Microsoft Defender for Business)

Source: Intelliseal Defender for Business Baseline SOP v1.0 (most detailed source — used as authoritative reference) · Intune Basic Setup (Windows)

Confirm prerequisites before starting
Defender SOP 2
  • Defender for Business licenses assigned to all users/devices in scope.
  • Windows 10/11 devices enrolled in Intune.
  • Devices are Azure AD-joined or Hybrid-joined.
  • Admin access confirmed to Intune, Microsoft 365 Defender, and Entra ID.
Applies to Windows 10 and Windows 11 devices only.
๐Ÿ’ก Double-check actual license assignment, not just purchase: Microsoft 365 admin center > Billing > Licenses will show whether Defender for Business is assigned per-user, since a purchased-but-unassigned license won't onboard that user's device.
Onboard devices to Microsoft Defender for Endpoint
Defender SOP 3
Intune admin center → Endpoint security → Microsoft Defender for Endpoint → Onboarding
  1. First confirm "Connect Intune with Microsoft Defender for Endpoint" (Section 4) is turned on — onboarding depends on that connector.
  2. Create an onboarding policy.
  3. Set Onboarding = Onboard.
  4. Assign to the Pilot device group (or Intune-Windows-Devices once out of pilot — see the naming-consistency note in Section 4).
  5. Validate devices show as "Onboarded" in the Defender portal.
This pushes the sensor. It's separate from the "Win-EDR" configuration profile (Section 4) which sets EDR mode/telemetry — you need both, assigned to the same device group.
๐Ÿ’ก Modern Windows 10 (1709+) and Windows 11 use the streamlined onboarding method through Intune with no manual script needed. Only much older or non-Intune-managed devices need the classic onboarding package/script method.
Configure Antivirus baseline settings
mergedDefender SOP 4Intune Basic Setup
Intune admin center → Endpoint security → Antivirus
SettingRequired value
Real-time protectionEnabled
Behavior monitoringEnabled
Cloud-delivered protectionEnabled
Automatic sample submissionEnabled
PUA protectionBlock
Scan removable drivesEnabled
Tamper ProtectionEnabled
๐Ÿ”€ Conflict check — Antivirus: the Intune Basic Setup guide separately creates a simpler Antivirus profile ("Win-Defender": Cloud Protection = Allowed, Realtime Monitoring = Allowed, Submit Samples = send safe samples automatically). Don't deploy both as separate profiles — two Antivirus configuration profiles assigned to the same devices will show a Conflict status in Intune. Use this 7-setting baseline as the single authoritative Antivirus profile (it's the more complete one); if you already created the basic "Win-Defender" profile, delete or disable it, and set that duplicate control to "Not yet configured" in the Microsoft 365 Baseline Security Policy document until it's merged in here.
The Intune Basic Setup document also mentions a further "Configure Defender Antivirus (Enhanced)" hardening step, but the copy you provided cuts off before listing those settings. Treat the 7-setting baseline above as authoritative until that missing section is supplied.
๐Ÿ’ก After deploying, verify real-time protection is actually working using the EICAR test file (a harmless industry-standard string that all antivirus engines are designed to flag) instead of testing with a real virus sample.
Configure Attack Surface Reduction (ASR) rules — Audit then Block
Defender SOP 5
Intune admin center → Endpoint security → Attack surface reduction

Phase 1 — Audit (run for 7–14 days):

  • Block credential stealing from LSASS
  • Block Office apps from creating child processes
  • Block Office apps from injecting code
  • Block process creations from PSExec and WMI
  • Use advanced protection against ransomware

Phase 2 — Block: after validating audit results show no false positives, switch all rules above to Block mode.

Never deploy ASR Block rules tenant-wide without first completing the audit phase (see Common Pitfalls).
๐Ÿ’ก Before flipping from Audit to Block, review Defender > Reports > Attack surface reduction rules for any hits against legitimate line-of-business software, so you can add a targeted exclusion instead of breaking that app outright.
Configure Endpoint Detection & Response (EDR)
mergedDefender SOP 6Setup SOP
Intune admin center → Endpoint security → Endpoint detection and response
  • EDR in block mode: Enabled
  • Automatic investigation: Enabled
  • Automatic remediation: Enabled
Verify device-group scoping: ensure the assigned group (e.g. "MDATP") includes 100% of managed devices, not just the pilot set. See the naming-consistency check under "Create the Intune device group" in Section 4 — standardise on one group name across onboarding, EDR, AV, ASR and compliance so nothing is silently under-scoped.
๐Ÿ’ก "Block mode" lets Defender Antivirus act on EDR detections even when another vendor's antivirus is the primary (passive mode) protection — this is particularly useful if you're migrating away from a third-party AV gradually.
Configure Web & Ransomware Protection
Defender SOP 7
Intune admin center → Endpoint security → Antivirus / Attack surface reduction (Web protection & Ransomware protection sections)

Web Protection

  • Network protection: Block
  • SmartScreen: Block malicious and unwanted content

Ransomware Protection

  • Controlled Folder Access: start in Audit, then move to Block
  • Protect common user folders only
๐Ÿ”€ Conflict check — SmartScreen: the Intune Basic Setup guide's "Win-Basic-Settings" configuration profile (Section 4) also enables SmartScreen through the Settings Catalog. If both policies are assigned to the same devices, check Intune for a Conflict status; keep SmartScreen configured in only one place and set the other to "Not yet configured" in the Microsoft 365 Baseline Security Policy document.
๐Ÿ’ก Controlled Folder Access can flag legitimate software (some backup tools, older PDF editors, niche line-of-business apps) as unauthorized writers to protected folders. Keep an allow-list ready to add exceptions quickly during the audit phase rather than disabling the feature.
Run Defender validation & monitoring checks
Defender SOP 9
security.microsoft.com → Device inventory / Vulnerability management

Defender portal checks

  • Device status = Active
  • Sensor health = Healthy

Vulnerability management

  • No unresolved High exposure recommendations
  • Secure Score trending upward
๐Ÿ’ก For a fleet-wide health check in one pass, export the Defender portal's device inventory to CSV rather than clicking through devices individually — much faster once you're past a handful of machines.
Follow staged deployment strategy for Defender policies
Defender SOP 10
  1. Pilot group (IT & test users)
  2. Staged rollout (20–30% of devices)
  3. Full deployment
๐Ÿ’ก As a rough guide: 1–2 weeks in pilot, 2 weeks for the staged rollout, then full deployment — extend each phase for a larger or more risk-averse organisation.
Review common pitfalls before sign-off
Defender SOP 11
  • Skipping the ASR audit phase
  • Overusing exclusions
  • Disabling Tamper Protection
  • MFA not enforced
  • Treating antivirus alone as sufficient protection
Confirm Defender rollout completion criteria
Defender SOP 12
  • All devices onboarded
  • Tamper Protection enforced
  • ASR rules in Block mode
  • EDR in block mode enabled
  • MFA enforced tenant-wide

6. Data Protection & Compliance (Purview)

Source: Setup SOP (Step 5, 8) · Baseline Policy (4.4, 4.5)

Apply baseline Data Loss Prevention (DLP) rules for email & files
mergedBaseline Policy 4.4Setup SOP
purview.microsoft.com → Data loss prevention → Policies → Create policy
  1. Use built-in templates covering financial information and personal information (PII).
  2. Scope to Exchange, SharePoint, OneDrive, Teams.
  3. Start in test mode with policy tips before enforcing blocks.
๐Ÿ’ก Run new DLP policies in test/simulation mode (policy tips shown to users, nothing actually blocked) for at least a week before switching to enforce, so you catch false positives on legitimate business correspondence first.
Apply Sensitivity Labels to classify and protect data
mergedBaseline Policy 4.4Setup SOP
purview.microsoft.com → Information protection → Labels
  1. Create label taxonomy (e.g. Public, Internal, Confidential, Highly Confidential).
  2. Publish a label policy to the relevant users/groups.
  3. Requires appropriate licensing (Business Premium/E5 compliance add-on).
๐Ÿ’ก Publish a default label (e.g. "Internal") that applies automatically to new content, so nothing is left completely unlabeled while users get used to picking labels themselves.
Configure Retention Policies for email, SharePoint, OneDrive
mergedSetup SOPBaseline Policy 4.5
purview.microsoft.com → Data lifecycle management → Retention policies
  1. Set retention duration in line with company/regulatory requirements.
  2. Apply defaults for the Recycle Bin as well as long-term retention where required.
๐Ÿ’ก Retention takes precedence over deletion: if a user deletes an item that's under a retention policy, it's preserved in a hidden recoverable location for the remainder of the retention period rather than being permanently gone.
Enable Unified Audit Log
mergedBaseline Policy 4.5Setup SOP
purview.microsoft.com → Audit → Start recording user and admin activity
  1. Enable audit logging tenant-wide if not already on.
  2. Confirm search returns results for a recent test action.
๐Ÿ’ก Very recent activity can take up to 30 minutes to appear in audit log search results — if a search comes back empty right after an event, wait and re-run it before assuming logging isn't working.
Configure eDiscovery
Setup SOP
purview.microsoft.com → eDiscovery
  1. Set up an eDiscovery (Standard or Premium, per licence) case for the tenant.
  2. Assign case admins/investigators.
๐Ÿ’ก Standard eDiscovery cases are included at no extra cost in Business Premium/E3. eDiscovery Premium (review sets, analytics, custodian management) needs E5 or the compliance add-on.
Enable Litigation Hold for key mailboxes
Setup SOP
Exchange admin center → Recipients → Mailboxes → select mailbox → Other settings → Litigation hold
  1. Identify key mailboxes requiring hold (executives, finance, legal).
  2. Enable litigation hold and set duration (or indefinite).
๐Ÿ’ก The default litigation hold duration isn't indefinite unless you explicitly set it that way — use an unlimited/0 duration if the actual requirement is to preserve mail regardless of user action for as long as the mailbox exists.
Turn on OneDrive Known Folder Move/Backup (Desktop, Documents, Pictures)
mergedBaseline Policy 4.4Setup SOP
admin.onedrive.com → Sync → Known Folder Move, or Intune configuration profile
  1. Enable Known Folder Move for Desktop, Documents, and Pictures.
  2. Notify users to complete the redirect prompt on first sign-in.
๐Ÿ’ก Enabling Known Folder Move on a device with a large existing Desktop/Documents folder can take hours for the initial upload — consider scheduling the rollout outside business hours for users with a lot of local data.
Review sign-in logs and risk reports; enable sign-in risk email alerts
mergedSetup SOPBaseline Policy 4.5
Entra admin center → Identity → Monitoring & health → Sign-in logs / Identity Protection
  1. Review risky sign-ins and risky users reports periodically.
  2. Configure email notifications to admins for risk detections (requires Identity Protection).
๐Ÿ’ก Viewing sign-in logs is included at every tier, but automated risk-based Conditional Access policies (blocking on "risky sign-in") need Entra ID Identity Protection, which is a P2 feature — check your licensing if you want that automation rather than manual log review.

7. SharePoint & OneDrive Configuration

Source: M365 Business Premium Setup Package

Configure SharePoint sites (Team sites / Communication sites)
Setup Package
admin.microsoft.com → SharePoint admin center → Sites → Active sites → Create
  1. Create a Team site per department/project that needs its own document library and Team.
  2. Create a Communication site for company-wide announcements/intranet content.
  3. Set site owners and default permission groups.
๐Ÿ’ก The default SharePoint storage pool is 1TB for the tenant plus roughly 10GB per licensed user, shared across every site — keep an eye on total usage as you create more sites.
Set SharePoint external sharing policies
Setup Package
SharePoint admin center → Policies → Sharing
  1. Set the organisation-wide default (e.g. "New and existing guests" rather than "Anyone" links, unless the business genuinely needs anonymous links).
  2. Review per-site sharing settings for anything more sensitive than the default (finance, HR, exec sites).
๐Ÿ’ก If you can't fully disable "Anyone" links, set them to expire automatically (e.g. after 30 days) as a middle-ground that still allows quick external sharing without leaving links open indefinitely.
Configure OneDrive storage limits and sync restrictions
Setup Package
admin.onedrive.com → Storage / Sync
  1. Set the default OneDrive storage quota per user (up to the Business Premium 1TB entitlement).
  2. Restrict sync to domain-joined/managed devices only (block sync on unmanaged/personal PCs) if required by policy.
Known Folder Move / Backup and document retention/versioning for OneDrive & SharePoint are covered in Section 6 (Data Protection & Compliance) to keep all Purview-managed settings together — don't configure retention twice.
๐Ÿ’ก Business Premium includes 1TB of OneDrive storage per user by default; this can be increased from the SharePoint admin center's storage settings if a user genuinely needs more.

8. Microsoft Teams & Outlook

Source: Setup SOP (Step 6) · M365 Business Premium Setup Package

Configure Microsoft Teams (structure, meeting policies, guest access, naming)
mergedSetup SOPSetup Package
admin.teams.microsoft.com
  1. Set up initial Teams structure by department/project.
  2. Apply a naming convention for new Teams (e.g. prefix by department/project code) via Teams naming policy.
  3. Configure meeting policies: who can record meetings, transcription, and default meeting settings.
  4. Configure external access (federation with other domains) and guest access separately — decide whether guests can be added to Teams at all, and if so, what they can see.
  5. Apply messaging and app-permission policies as required.
๐Ÿ’ก Guest access and external access are two different settings people often mix up: external access (federation) lets people from other Microsoft 365 tenants find and message your users; guest access lets you add specific external individuals into your Teams and channels directly.
Configure Outlook default signature and mail policies
Setup SOP
Exchange admin center → Mail flow → Rules (disclaimer/signature rule)
  1. Create a transport rule to append a standard signature/disclaimer.
  2. Set organisation-wide mail policies as required.
๐Ÿ’ก Set the disclaimer/signature through a mail flow rule rather than per-client signatures, so messages sent from mobile, webmail, or shared mailboxes get the same disclaimer consistently, not just desktop Outlook.

9. User Onboarding

Source: Setup SOP (Step 7)

Create user accounts in the Admin Center
Setup SOP
admin.cloud.microsoft → Users → Active users → Add a user
๐Ÿ’ก For onboarding multiple people at once, the admin center supports a bulk CSV upload of new users instead of creating accounts one at a time.
Assign licenses and role-based access
Setup SOP
admin.cloud.microsoft → Users → select user → Licenses and apps / Roles
๐Ÿ’ก Consider group-based licensing (assign the license to a security group, not each user individually) so new hires added to the group automatically inherit the correct license set.
Send login credentials and onboarding instructions
Setup SOP

Deliver temporary credentials securely and require password + MFA registration at first sign-in.

๐Ÿ’ก Use the admin center's auto-generated temporary password with "require password change at first sign-in" enabled, rather than reusing the same temporary password across multiple new hires.
Train users on Teams, OneDrive, and Outlook
Setup SOP

Provide a short onboarding session or quick-reference guide covering daily use of Teams, OneDrive, and Outlook, plus how to register MFA methods.

๐Ÿ’ก A short one-page cheat-sheet handed out alongside live training (covering Teams, OneDrive, Outlook basics and how to register MFA) tends to get referenced far more often than people re-attending or re-watching a training session.

10. Backup & Disaster Recovery

Source: Setup SOP (Step 8)

Schedule regular third-party backup for Teams, SharePoint, and Exchange
Setup SOP
  1. Select a third-party backup provider (e.g. Acronis, Datto).
  2. Configure backup scope: Exchange mailboxes, SharePoint sites, OneDrive, Teams data.
  3. Set backup frequency and retention, and periodically test a restore.
๐Ÿ’ก Follow the 3-2-1 rule as a rule of thumb: at least 3 copies of the data, on 2 different types of storage, with 1 copy offsite. Microsoft's native retention/recycle bin features are not a substitute for a real backup — they don't fully protect against malicious or accidental permanent deletion the way a separate backup does.

11. Governance: Exceptions & Review Cadence

Source: Baseline Policy (5, 6)

Document and approve any security exceptions
Baseline Policy 5
  • Any request to disable MFA, legacy authentication, or mailbox protections must be documented and approved by the Security Lead.
  • Exceptions expire after 90 days unless reapproved.
๐Ÿ’ก Keep a simple exceptions register (even a spreadsheet) logging who requested the exception, who approved it, and its expiry date, so the 90-day reapproval requirement doesn't get missed.
Set up ongoing verification & maintenance cadence
Baseline Policy 6
  • Initial setup checklist completed and signed off by the IT Engineer.
  • Quarterly review of tenant Secure Score, audit logs, and compliance alerts.
  • Annual policy review to align with current Microsoft recommendations.
๐Ÿ’ก Put the quarterly and annual reviews on a recurring calendar invite with this checklist linked, rather than relying on someone remembering to schedule it manually.