How to Audit Your Microsoft 365 Security in 2026 (Complete Guide)

Most small and mid-sized businesses using Microsoft 365 assume they're secure by default. They're not. Out-of-the-box M365 configurations leave dozens of critical security gaps — gaps that attackers actively exploit.

This guide walks you through what a proper Microsoft 365 security audit covers, what to look for, and how to fix the most common misconfigurations before they become incidents.

Why Microsoft 365 Security Audits Matter

Microsoft 365 is the productivity backbone of over 300 million business users worldwide. That makes it the single most targeted platform for phishing, credential theft, and business email compromise (BEC) attacks.

According to Microsoft's own threat intelligence, over 80% of ransomware attacks enter through identity-related weaknesses — most of which are preventable through proper M365 configuration.

An audit doesn't just find problems. It gives you a prioritized remediation plan, helps you meet compliance requirements (ISO 27001, GDPR, NIS2), and protects your business from the most common attack vectors.

What Does a Microsoft 365 Security Audit Cover?

A thorough M365 security audit evaluates your tenant against industry benchmarks — primarily the CIS Microsoft 365 Foundations Benchmark — across these key areas:

1. Identity & Access Management

Are Multi-Factor Authentication (MFA) policies enforced for all users?
Are there accounts with Global Administrator privileges that don't need them?
Is legacy authentication (basic auth) disabled?
Are Conditional Access policies in place?

2. Email Security

Is Microsoft Defender for Office 365 configured correctly?
Are anti-phishing, anti-spam and Safe Links policies active?
Is DMARC, DKIM and SPF configured for your domain?

3. Data Protection

Are sensitivity labels applied to confidential data?
Is Data Loss Prevention (DLP) enabled?
Are external sharing settings in SharePoint and OneDrive appropriately restricted?

4. Audit Logging & Monitoring

Is the Unified Audit Log enabled?
Are sign-in logs being monitored for suspicious activity?
Are alerts configured for high-risk events?

5. Device & Endpoint Security

Are devices enrolled in Intune or compliant with your device policies?
Is Microsoft Secure Score being tracked?

The 5 Most Critical Microsoft 365 Misconfigurations

Based on thousands of tenant scans, these are the issues we see most often:

❌ 1. MFA Not Enforced

Legacy per-user MFA settings are frequently misconfigured or inconsistently applied. Modern Conditional Access policies should enforce MFA for all users, especially admins.

❌ 2. Too Many Global Admins

The principle of least privilege is regularly violated. Most tenants have 3-5x more Global Admins than necessary. Each one is a high-value target.

❌ 3. Legacy Authentication Enabled

Protocols like IMAP, POP3 and basic SMTP don't support MFA. As long as they're enabled, an attacker with a stolen password can bypass MFA entirely.

❌ 4. Security Defaults Disabled Without Replacement

Security Defaults provide a basic security baseline. Many tenants disable them to configure Conditional Access — but never complete the Conditional Access setup, leaving a gap.

❌ 5. Audit Logging Turned Off

Without audit logging, you have no visibility into who did what, and when. This also makes compliance reporting (GDPR, ISO 27001) nearly impossible.

How Long Does a Manual M365 Audit Take?

A thorough manual audit of a Microsoft 365 tenant typically takes 40 to 80 hours for an experienced IT security consultant. That includes:

Reviewing all policy configurations
Cross-referencing against CIS Benchmark controls
Documenting findings
Writing remediation recommendations

For most SMBs, this means expensive external consultants or weeks of internal IT time — just to get a point-in-time snapshot that's outdated the moment configurations change.

Automate Your Microsoft 365 Security Audit with SecureTenant

SecureTenant was built specifically to solve this problem for SMBs. Instead of 40+ hours of manual work, SecureTenant scans your entire Microsoft 365 tenant in under 5 minutes — automatically checking against CIS Benchmarks, Microsoft Security Defaults, and compliance frameworks including ISO 27001, GDPR and NIS2.

Here's what you get:

Automated scan of your full M365 tenant configuration
Prioritized findings sorted by severity (Critical, High, Medium, Low)
One-click remediation scripts for the most common issues
Compliance mapping to GDPR, ISO 27001 and NIS2 requirements
Read-only access — SecureTenant never writes to your tenant
EU data residency — all data processed and stored in Azure West Europe

No consultant needed. No weeks of waiting. Just a clear, actionable security report in minutes.

Getting Started

A Microsoft 365 security audit doesn't have to be a months-long project. The most important thing is to start — identify your current gaps, prioritize the critical ones, and work through them systematically.

If you want to see where your tenant stands today, run a free scan with SecureTenant and get a high-level overview of your most critical vulnerabilities in under 5 minutes.

SecureTenant is a Microsoft 365 security scanning platform built for IT Managers and CISOs at SMBs. Read-only, GDPR compliant, EU data residency.