How to Automate CIS Checks for Microsoft 365

Trying to secure Microsoft 365 just by clicking around the admin centers is a losing battle.

You’ve got:

• Entra ID (Azure AD)
• Exchange Online
• SharePoint Online
• OneDrive
• Microsoft Teams
• Intune / Endpoint Manager
• Conditional Access, Defender, and more

Every one of these has dozens (sometimes hundreds) of security-relevant configuration options. Manually checking them for a microsoft 365 security audit usually leads to:

• Missed risky settings (for example legacy auth still enabled somewhere)
• Inconsistent checks between admins
• Zero repeatability — you can’t easily prove to auditors what you actually checked and when

In my experience, this is exactly how “we thought that was turned off” ends up in an incident report.

Automated compliance m365 testing solves this by:

• Running the same set of checks every time
• Providing clear pass/fail results
• Producing reports you can hand to auditors or management

The CIS Microsoft 365 Foundations Benchmark is a widely recognised baseline for securing Microsoft 365. It defines a set of controls and recommendations (for example number of Global Admins, MFA requirements, logging configuration) that strongly influence your overall security posture.

Auditors and security assessors love CIS because:

• It’s vendor-neutral and openly documented
• It maps well to other frameworks (NIST CSF, ISO 27001, etc.)
• It gives a clear “good practice” yardstick

So if you’re wondering how to prepare for microsoft 365 security audit, aligning with CIS benchmark microsoft 365 is one of the most effective first moves you can make.

The challenge is: how do you actually check all those CIS controls without spending weeks digging through every admin blade? That’s where security test automation frameworks like Meister — and more advanced microsoft 365 compliance automation tools — really shine.

To run automated tests, you’ll need a few basics in place:

1. A Windows machine (or server) with PowerShell 7
Meister relies on modern PowerShell, so make sure PowerShell 7 is installed.

2. Network access to Microsoft 365
The machine needs outbound HTTPS access to your tenant services (Entra ID, Exchange Online, SharePoint, etc.).

3. An account with appropriate permissions
Typically a Global Administrator is used for the initial setup, because the framework needs to query configuration across multiple services. For ongoing use, you might create a dedicated “assessment” account with just enough rights.

4. A working folder
Create a simple folder, for example:

• `C:\Meister`

This is where test definitions and reports will live.

It sounds basic, but getting these lined up up-front saves a lot of friction later, especially when you automate this in a scheduled way.

Meister uses Pester (a popular PowerShell testing framework) under the hood. You install both from the PowerShell Gallery.

From an elevated PowerShell 7 session:

```powershell
Set-Location C:\Meister

Install-Module -Name Pester -Scope CurrentUser
Install-Module -Name Meister -Scope CurrentUser
```

That’s the whole installation for the modules. Nothing too fancy here.

After this, you need to initialise the tests so they live on disk and can be customised.

```powershell
Invoke-MeisterInit
```

This will create a `Tests` folder under `C:\Meister` (or the current directory) and populate it with a large set of test files. Inside you’ll see folders for things like:

• `Exchange`
• `Entra`
• `Teams`
• `SharePoint`
• and special folders for CIS or CISA-based tests

These files are essentially your automated m365 compliance assessment rules, which you can review and extend as needed.

Meister provides a helper command that signs into the key Microsoft 365 services for you.

From your PowerShell 7 window in `C:\Meister`:

```powershell
Invoke-MeisterConnect
```

You’ll be prompted with sign-in windows for:

• Entra ID / Azure AD
• Exchange Online
• SharePoint Online
• Teams

Use your Global Admin (or delegated assessment) account for each prompt. Once authenticated, Meister can query your configuration across these workloads.

To be honest, this is the point where many admins realise just how many services they’re actually responsible for, because it walks you through each one.

Now for the interesting bit: running the full test suite.

In the same session, run:

```powershell
Invoke-Meister
```

Meister will:

• Execute over 280 security tests across your tenant
• Cover Entra ID, Exchange Online, SharePoint, Teams, Conditional Access and more
• Include CIS microsoft 365 foundations checks, CISA checks, and Meister’s own built-in tests

This can take a few minutes, depending on tenant size. At the end, you’ll see a summary similar to:

• Total tests: 280
• Passed: 113 (44%)
• Failed: 143
• Not Tested: 24

Numbers will vary, but don’t be surprised if your first run looks worse than you expect. That’s normal. It simply means you now have visibility instead of a false sense of security.

Meister also produces an interactive HTML-style report (or console output, depending on your config) that you can open to explore each finding.

In the report, each test typically includes:

• Test ID (often indicating the profile, e.g., CIS)
• Title – what control or setting is being checked
• Severity – Low, Medium, High, etc.
• Status – Passed, Failed, Not Tested
• Info/Details – why it failed or passed
• Remediation guidance – steps or links to fix it

Useful ways to work with the report:

1. Filter by category
Filter to CIS controls if your priority is the cis benchmark microsoft 365 guide aspect, or to “built-in” Meister tests for broader hygiene checks like conditional access or spam policies.

2. Filter by status = Failed
This gives you a focused to-do list. These are your current gaps.

3. Sort by severity
Start with High and Critical items. For example, you might see:

• “Ensure that between two and four Global Admins are designated” – High
• “Conditional Access policy to require MFA for risky sign-ins” – High

4. Use the remediation info
Most tests provide clear remediation steps and sometimes direct Microsoft Learn links. Instead of hunting around the portal, you can follow a guided path to fix issues.

This is where the framework really pays off: it turns a vague “we should improve security” into a concrete, prioritised backlog.

For microsoft 365 audit preparation, documentation is half the battle. You need to show not only that you care, but that you systematically test, detect, and remediate.

Meister supports exporting results to CSV or Excel. From there you can:

• Feed results into Power BI dashboards
• Track remediation progress over time
• Attach evidence to internal risk registers or tickets
• Provide snapshots during an m365 security audit

In practice, I recommend:

• Exporting the full result set after each run
• Keeping them in a central, access-controlled location
• Tagging each file with date and profile (e.g. `Meister-CIS-Assessment-2026-03-10.xlsx`)

This simple habit gives you a lightweight, defensible history of your automated m365 compliance assessment activity.

Meister can be integrated with various automation services to run on a schedule, such as:

• Windows Task Scheduler
• Azure Automation
• GitHub Actions or Azure DevOps pipelines

The pattern is roughly:
1. Connect to Microsoft 365 (non-interactive auth, if appropriate)
2. Run `Invoke-Meister`
3. Export results
4. Email or push results into Teams

The docs show how you can:

• Send email alerts when tests fail or when a threshold is crossed
• Post Teams notifications with summary results

This turns your m365 compliance checklist from a dusty spreadsheet into a living process. When something drifts — say, a new Global Admin is added, or a risky policy gets relaxed — you can be alerted and react before an auditor, or worse an attacker, finds it.

This is the essence of automated compliance m365:

• Continuous checking
• Fast detection of drift
• Repeatable evidence

An open-source framework like Meister is fantastic for:

• Getting quick visibility at low cost
• Learning what “good” looks like
• Building your first automated m365 security assessment pipeline

However, as your organisation matures, you’ll probably need:

• Formal CIS certification of the assessment method
• Profile support (CIS Level 1 vs Level 2)
• Control mapping to other standards (NIS2, ISO/IEC 27001, SOC 2, HIPAA, PCI DSS, NIST CSF)
• Audit-ready PDF reports with embedded evidence
• Fine-grained RBAC for security and compliance teams
• Configuration drift detection in near real-time

That’s where specialised microsoft 365 compliance automation tools enter the picture. One example in the Microsoft ecosystem is ConfigCobra, which is available via Microsoft AppSource and focuses specifically on automated, CIS-certified Microsoft 365 compliance assessments.

ConfigCobra continuously checks Microsoft 365 against 129 CIS Microsoft 365 Foundations Benchmark controls, supports Level 1 and Level 2 profiles, and generates audit-ready reports with remediation guidance. It also supports scheduled assessments (daily, weekly, monthly), real-time drift detection, and custom rule sets mapped to multiple compliance standards.

So the pattern is often:

• Start with something like Meister to build familiarity and internal processes
• Move to a dedicated platform like ConfigCobra when you need enterprise-grade reporting, certifications, and cross-framework mapping