Microsoft 365 Security Assessment Checklist

How to manage SaaS risk in Microsoft 365 with security controls

Microsoft 365 is the backbone of modern work, supporting email, collaboration, file sharing, and identity for more than 3.7 million companies worldwide. That scale also makes M365 one of the most targeted SaaS platforms, where misconfigurations, overpermissioned accounts, and unmanaged integrations can quietly create serious security gaps.

Effective M365 security is more than turning features on. Companies need the right security controls in place to continuously assess risk, maintain visibility, and prevent configuration drift. Here’s a checklist of seven critical M365 security controls designed to protect data, reduce exposure, and support a stronger security posture:

1. Consistently Enforce Security Policies Across M365 Service

With a wide range of services—Teams, Exchange Online, SharePoint—M365 requires consistent security policies to ensure no weak points exist across your environment. Inconsistent policies can lead to vulnerabilities.

Key actions to take:

  • Regularly review and align security policies across all M365 services, ensuring they’re applied uniformly.
  • Set up alerts for deviations in policies to respond quickly to any security gaps.

2. Enforce Least Privilege Access for M365 Admin and User Roles

Over-permissioned accounts, especially admin roles, are a major risk in M365. Limiting access to only what’s necessary reduces the chances of internal misuse or external SaaS attacks leveraging compromised accounts.

Key actions to take:

  • Continuously audit role-based access controls (RBAC) in Azure AD, Power Pages, and SharePoint Online.
  • Implement automated workflows to ensure permissions are adjusted as user roles change.

3. Secure Third-Party App Integrations via OAuth in Microsoft 365

Third-party apps that connect to M365 via OAuth can introduce new vulnerabilities if left unchecked. It’s critical to manage and limit the  permissions granted to these apps to protect your M365 data.

Key actions to take:

  • Regularly audit third-party app permissions to ensure they only access the necessary data.
  • Restrict OAuth scopes to minimize exposure, particularly in Teams, OneDrive, and SharePoint.

4. Limit External Data Sharing in SharePoint and OneDrive

SharePoint and OneDrive are core collaboration tools in M365, but misconfigured sharing settings can lead to data exposure. Managing these settings is essential to protecting sensitive information from being accessed by the wrong people.

Key actions to take:

  • Regularly review external sharing settings in SharePoint and OneDrive to prevent unauthorized access. 
  • Enforce Data Loss Prevention (DLP) policies to protect sensitive information from accidental data leakage.

5. Lock Down High-Risk Configuration Settings in Microsoft 365

Certain settings, like PowerShell access and global admin permissions, represent higher security risks if not properly controlled. Configuration drift in these areas can silently weaken your security posture over time, creating vulnerabilities without immediate signs of danger.

Key actions to take:

  • Secure high-risk configurations like mailbox forwarding rules, PowerShell access, and API permissions. 
  • Enable alerts for any changes to critical settings, allowing for quick detection, and remediation.

6. Use Microsoft 365 Audit Logs for Early Threat Detection

Audit logs in M365 track user activities and configuration changes, making them crucial for spotting suspicious behavior before it escalates. Proactively monitoring these logs helps detect threats early and enables swift responses.

Key actions to take:

  • Continuously monitor M365 audit logs for signs of suspicious activity, such as unauthorized login attempts or unusual file access. 
  • Set up custom alerts for high-risk actions, such as changes to administrative privileges or external sharing in Teams and OneDrive.

7. Run Continuous Compliance Audits for Regulatory Standards

For organizations bound by regulations like GDPR, SOC2, or HIPAA, staying compliant is essential. Continuous audits of your M365 environment ensure  you meet requirements and avoid costly penalties.

Key actions to take:

  • Automate compliance scans to ensure security settings align with regulatory standards. 
  • Generate regular reports to demonstrate adherence to industry requirements.

Manually monitoring Microsoft 365 activity at scale is complex. AppOmni simplifies Microsoft 365 security by turning expanded audit logs into actionable detections.

With AppOmni, security teams can:

  • Automate monitoring and alerting for security events across M365 and other SaaS applications, reducing manual work.
  • Apply customizable detection rules without needing complex queries or specialized expertise.
  • Correlate activity across multiple SaaS platforms to identify meaningful patterns and real threats faster.
  • Integrate with SIEM and SOAR solutions to streamline workflows and simplify response efforts.
  • Conduct automated compliance checks that make meeting industry standards like NIST, ISO 27001, and SOC 2 easier.

With built-in expertise, clear guidance, and automation, AppOmni makes securing SaaS environments easier and more effective than ever.

Download Microsoft 365 Security Assessment Checklist Now.