Microsoft 365 Security Baseline Implementation

Introduction

A properly secured Microsoft 365 tenant is the foundation of modern enterprise security. This project walks through implementing a comprehensive security baseline aligned with CIS Benchmarks and Microsoft's own security recommendations.

What You'll Build

• Identity protection with conditional access and PIM
• Email security hardening (anti-phishing, DMARC, safe links)
• Endpoint management with Intune compliance policies
• Data governance with sensitivity labels and DLP
• Audit logging and security monitoring
• Compliance dashboard with automated scoring

Who This Is For

• IT administrators responsible for M365 security
• MSP engineers standardizing client tenant configurations
• Security teams implementing compliance frameworks
• Organizations preparing for SOC 2, HIPAA, or PCI DSS audits

Time to complete: 8-12 hours (phased implementation recommended)

Prerequisites

License Requirements

Required Roles

• Global Administrator (initial setup only)
• Security Administrator
• Exchange Administrator
• Compliance Administrator
• Intune Administrator

Project Phases

Phase 1: Identity Security          [Day 1]     ████████████░░░ 40%
Phase 2: Email Security             [Day 1-2]   ██████████████░ 60%
Phase 3: Endpoint Management        [Day 2-3]   ████████████████ 75%
Phase 4: Data Governance            [Day 3-4]   ████████████████ 90%
Phase 5: Monitoring & Compliance    [Day 4-5]   ████████████████ 100%

Phase 1: Identity Security

1.1 Emergency Access Accounts

Create two break-glass accounts before configuring any policies:

1.2 Conditional Access Policies

Deploy in this order (each policy should be tested in Report-only mode for 24-48 hours before enforcing):

Policy 1 — Require MFA for All Users:

• Target: All users (exclude break-glass accounts)
• Cloud apps: All cloud apps
• Grant: Require authentication strength — Phishing-resistant MFA
• Session: Sign-in frequency — 12 hours

Policy 2 — Block Legacy Authentication:

• Target: All users
• Cloud apps: All cloud apps
• Conditions: Client apps — Exchange ActiveSync, Other clients
• Grant: Block

Policy 3 — Require Compliant or Hybrid Joined Device:

• Target: All users
• Cloud apps: Office 365
• Grant: Require device to be marked as compliant OR Require Hybrid Azure AD joined device

Policy 4 — Restrict Admin Portal Access:

• Target: All users (exclude Global Admins)
• Cloud apps: Microsoft Admin Portals
• Grant: Require MFA + compliant device

Policy 5 — Block High-Risk Sign-ins:

• Target: All users
• Conditions: Sign-in risk — High
• Grant: Block

Policy 6 — Require Password Change for High-Risk Users:

• Target: All users
• Conditions: User risk — High
• Grant: Require MFA + require password change

1.3 Privileged Identity Management (PIM)

Configure just-in-time admin access:

Phase 2: Email Security

2.1 Domain Authentication

2.2 Anti-Phishing

Configure the Strict preset security policy in Microsoft 365 Defender, which sets:

• Mailbox intelligence protection: Quarantine
• Spoof intelligence: Enabled
• First contact safety tips: Enabled
• Impersonation protection for executives and key partners

2.3 Transport Rules

Phase 3: Endpoint Management (Intune)

3.1 Device Compliance Policies

Windows 10/11 Compliance:

macOS Compliance:

3.2 Device Configuration Profiles

Windows Security Baseline:

3.3 Windows Autopilot

Configure for zero-touch deployment:

1. Register device hardware IDs
2. Create Autopilot deployment profile
3. Assign to device group
4. User-driven or self-deploying mode

Phase 4: Data Governance

4.1 Sensitivity Labels

4.2 Data Loss Prevention Policies

4.3 Retention Policies

Phase 5: Monitoring and Compliance

5.1 Audit Configuration

• Enable Unified Audit Log
• Enable Mailbox Auditing (all mailboxes, 365-day retention)
• Enable Advanced Audit (E5) for critical accounts
• Configure audit log search access (Security team only)

5.2 Alert Policies

5.3 Microsoft Secure Score

Target these quick wins first:

Implementation Checklist

Identity

• Break-glass accounts created and documented
• MFA enforced for all users (phishing-resistant for admins)
• Legacy authentication blocked
• Conditional access policies deployed and enforced
• PIM configured for privileged roles
• Self-service password reset enabled

Email

• SPF, DKIM, DMARC configured
• Anti-phishing policies at strict preset
• Safe Links and Safe Attachments enabled
• External email banner active
• Auto-forwarding blocked
• Dangerous attachment types blocked

Endpoints

• Compliance policies deployed for all platforms
• BitLocker/FileVault required
• Defender AV and ASR rules configured
• Windows Update policies set
• Autopilot configured for new devices

Data

• Sensitivity labels published
• DLP policies active
• Retention policies configured
• External sharing restricted

Monitoring

• Unified audit log enabled
• Alert policies configured
• Secure Score reviewed and actions tracked
• Quarterly compliance review scheduled

References

• CIS Microsoft 365 Foundations Benchmark
• Microsoft Security Documentation
• Microsoft Secure Score
• NIST SP 800-171 — Protecting CUI