Microsoft 365 Security Audit Guide: Steps, Tips & Best Practices
A Microsoft 365 security audit is one of the best ways to check whether your cloud setup is safe, compliant, and ready to face modern threats.
Many organizations use Microsoft 365 daily but often forget to review the security settings that protect their environment—especially after projects like office 365 migration services, new deployments, or user onboarding.
Running a proper audit helps you uncover risks, understand how attackers might enter, and take quick action to fix weak spots.
Key Takeaways
- A Microsoft 365 security audit helps identify risks before they become serious issues.
- It checks configuration, access rights, compliance, and baseline security controls.
- An audit improves your Microsoft Secure Score and helps meet GDPR, HIPAA, or other standards.
- You receive actionable remediation steps to strengthen your environment.
- This process protects your users, data, and business from evolving threats.
What Is a Microsoft 365 Security Audit?
A Microsoft 365 security audit is a full assessment of your cloud tenant, covering user access, configurations, applications, and compliance settings.
The goal is to spot security gaps and strengthen your environment while also eliminating unused or unnecessary services for better cloud cost management.
Key tools and areas reviewed include:
- Identity protection
- Mail and data loss controls
- SharePoint/OneDrive sharing rules
- Admin roles & permissions
- Threat protection and Defender settings
Why a Microsoft 365 Security Audit Matters
A security audit directly reduces cyber risks and strengthens how your team works.
Benefits include:
- Reduced cyber risk
- Stronger productivity
- Better data protection
- Compliance alignment
Key Elements of a Microsoft 365 Security Audit
A complete audit covers all components that influence your security posture:
- Identity & access checks
- Mail & data safety
- Device & app controls
- Compliance & governance
Steps to Conduct a Microsoft 365 Security Audit
Below is a simple and structured guide to help you run your audit effectively.
1. Start With Your Security Baseline
Your security baseline is the starting point for understanding current strengths and weaknesses.
Checklist:
- Review admin roles
- Review sign-in logs
- Review baseline security policies
- Review MFA and authentication settings
2. Review Identity and Access Controls
Identity is the foundation of cloud security.
Focus on how users sign in and what resources they can access.
What to check:
- MFA setup
- Conditional Access policies
- Password policies
- Guest/external access
- High-risk or privileged accounts
3. Review Mail, SharePoint, and OneDrive Security
Email and file sharing are major attack vectors.
Review these areas to prevent phishing, data leakage, and malware infiltration.
Items to review:
- Safe Links
- Safe Attachments
- External sharing settings
- Mail flow rules
- Anti-spam & anti-malware policies
- License & usage compliance (ensuring license compliance in Microsoft 365)
4. Check Device and App Security
Organizations often use multiple devices across various locations.
Ensure all endpoints follow security rules.
Audit focus areas:
- Device compliance rules
- App protection policies
- Device enrollment status
- Access from unmanaged devices
- Removing risky or unused apps
5. Review Threat Protection Settings
Microsoft Defender includes core tools to block phishing, malware, and suspicious activity.
Key tools to review:
- Microsoft Defender policies
- Anti-phishing policies
- Real-time threat detection
- Attack simulation training
- Safe Attachments configuration
6. Review Microsoft 365 Compliance Center Settings
Tools such as the Microsoft 365 Compliance Center help ensure your tenant follows regulatory and internal rules.
Compliance areas:
- Retention policies
- Legal holds
- Compliance Score
- Data classification
- Content search and audit rules
7. Review Logs, Reports, and Alerts
Audit logs reveal user activity, admin actions, and suspicious behavior.
Check these logs:
- Audit logs
- Admin activity logs
- Sign-in logs
- Exchange logs
- SharePoint logs
8. Create Remediation Plans
After completing your audit, create a prioritized remediation roadmap.
Your plan should include:
- Issue description
- Steps to fix
- Responsible person
- Priority level
- Expected results
Common Mistakes to Avoid
- Ignoring identity checks
- Using outdated email protection policies
- Granting too many admin rights
- Overlooking device compliance
- Skipping compliance reviews
Best Practices to Strengthen Microsoft 365 Security
- Enable MFA everywhere
- Use Conditional Access rules
- Review admin roles regularly
- Check Secure Score weekly
- Train users on phishing risks
- Use device management via Microsoft Intune (Mastering Microsoft Intune Setup Like a Pro)
- Configure Data Loss Prevention in Microsoft 365
- Prepare environments following how to prepare for a Microsoft 365 migration
- For telecom readiness, verify Microsoft Teams phone setup
Real Examples of Why Audits Matter
- Found five unused admin accounts—removed to prevent unauthorized access.
- Public file sharing detected—rules updated to secure customer data.
- Weak spam protection—improved policies blocked harmful emails.
Advanced Tips for a Stronger Audit
- Run audits twice a year
- Create standardized user access policies
- Review connected apps regularly
- Set automated alerts in the Compliance Center
- Follow CISA’s best practices and Microsoft
Conclusion
A Microsoft 365 security audit is simple, powerful, and essential.
It protects your data, improves your security score, and ensures compliance across your environment.
If you want help optimizing your Microsoft 365 setup, strengthening your Secure Score, or conducting a full audit —
contact our experts today to secure your environment.
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2025-12-09