🛡️ Microsoft Intune Security Baselines: What They Are, Which to Use, and How to Avoid Disrupting Productivity

If you’re managing Windows devices in Intune, one of the most overlooked but powerful tools at your disposal is Security Baselines. They let you apply Microsoft-recommended security configurations across your environment without having to build policies from scratch.

But here’s the reality: if you blindly apply them without understanding the impact, you’re going to break things. That’s why this guide cuts through the noise to help you understand which baselines to use, how to deploy them properly, and how to stay secure without making users miserable.

🔍 What Are Security Baselines?

A security baseline is a pre-configured set of device settings that Microsoft curates based on best practices and real-world threat intelligence. These baselines are designed to harden your environment against attacks while maintaining usability.

In Intune, these are deployed as configuration profiles and include categories like:

Microsoft Defender for Endpoint
Microsoft Edge
Windows 10/11 Security Baseline

🚦 Which Security Baselines Should You Use?

1. Windows 10/11 Security Baseline

This is your go-to for core Windows security settings like credential protection, user rights, account lockout policies, and more.

Best for: All environments — this should be your default starting point.

Things to watch: Can disable things like basic PowerShell or script behavior that your IT staff may rely on. Test first.

2. Microsoft Defender Antivirus Baseline

Targets antivirus settings, real-time protection, cloud-delivered protection, and attack surface reduction (ASR) rules.

Best for: Organizations using Defender for Endpoint or Business. Critical for blocking modern ransomware and malware techniques.

Things to watch: ASR rules can block legitimate tools — set to Audit Mode first if you’re unsure.

3. Microsoft Edge Baseline

Focuses on browser settings, like disabling outdated TLS versions, enforcing SmartScreen, and locking down dangerous browser behavior.

Best for: Organizations standardizing on Edge as the corporate browser.

Things to watch: May conflict with custom extensions or SSO behavior. Test with pilot users.

🧠 Best Practices: Deploy Without Breaking Productivity

1. Use Security Baselines in Audit Mode First

You can clone a baseline and set it to Audit Mode to see what would be enforced without enforcing it. This gives you insight into what settings may cause disruptions before they happen.

2. Assign to Pilot Groups

Don’t roll out to everyone on day one. Create pilot groups (IT staff, power users, or one department) and monitor closely. Get feedback.

3. Customize Baselines — Don’t Use as-Is

Microsoft gives you a solid base, but every org is different. Clone the baseline, tweak settings that conflict with business processes, then deploy.

Examples:

Disable ASR rules that block Office macros if your finance team still uses them.
Allow remote desktop if you use it for IT support.

4. Use Naming Standards and Versioning

Name your baselines clearly (e.g., Win10_SecBaseline_v1.2) and track versions. This makes it easier to troubleshoot or roll back changes later.

5. Document Exceptions

If you need to deviate from baseline settings (e.g., allowing PowerShell scripts for IT automation), log the reason and keep it reviewed. This helps with compliance and future audits.

💡 Real-World Deployment Tip

If you’re using Autopilot to onboard devices, apply baselines after provisioning is complete. This avoids failures during setup and gives users a cleaner out-of-box experience.

🚀 Final Thoughts

Intune Security Baselines are a fast way to boost security — but like any powerful tool, they can backfire if used recklessly. Start small, test thoroughly, and don’t be afraid to tweak. With a smart approach, you can lock down your environment without locking out your users.