Configure Endpoint Security with Microsoft Intune: Step-by-Step Guide


Configuring Endpoint Security with Microsoft Intune

Securing endpoints is one of the most important tasks for any organization using Microsoft Intune. By leveraging Endpoint Security policies, admins can apply consistent protection across devices without relying on manual configuration.

Recently, I reviewed a community walkthrough that demonstrated how to configure Microsoft Intune Endpoint Security settings. Below, I’ve expanded on those ideas and structured them into a step-by-step guide you can adapt for your own environment.


Why Use Endpoint Security in Intune?

Intune’s Endpoint Security node is designed for targeted security configurations. While you could apply many of these settings using configuration profiles, the Endpoint Security experience provides:

  • Simplified setup with security-focused templates
  • Clearer policy separation (e.g., Antivirus vs BitLocker vs Firewall)
  • Better reporting and troubleshooting visibility

This helps administrators maintain both compliance and a consistent security baseline.


Core Configurations to Deploy

Here’s a sample baseline configuration you can roll out with minimal effort:

1. Microsoft Defender Antivirus

  • Enable periodic scanning to catch threats on devices that may be running third-party AV.
  • Ensure real-time protection is active.
  • Consider cloud-delivered protection for faster signature updates.

2. Attack Surface Reduction (ASR) Rules

  • Start small. Apply one or two high-impact rules in audit mode first.
  • Example: Block executable content from email and webmail clients.
  • Review the logs before switching to enforcement.

3. Windows Security Experience

  • Configure the Windows Security app UX to ensure users can see their protection status.
  • Restrict access to advanced settings if you want admins to remain in full control.

4. BitLocker Drive Encryption

  • Enforce BitLocker on system drives for all Windows 10/11 endpoints.
  • Add a removable storage policy: deny writes to USB drives unless encrypted.
  • Store recovery keys in Azure AD for easy retrieval.

Testing Your Setup

After applying the policies, it’s critical to validate that protection is working as intended. One common method is running an EICAR test file:

  • This harmless test file is recognized as “malicious” by most antivirus software.
  • Deploy it to a test device to confirm Defender AV blocks access.
  • Review Intune’s reporting to ensure the event is logged.

This gives you confidence that the policy is active and functioning.


Things to Watch Out For

While these baseline configurations improve security, keep in mind:

  • Not all environments are alike. Blocking USB writes might disrupt workflows where external drives are required. Use pilot groups before broad rollout.
  • Balancing security and usability is key. Too many ASR rules can cause false positives or application issues.
  • Reporting and monitoring are as important as enforcement. Always check the logs before moving from audit to block.

Key Takeaways

  • Use Defender AV policies for baseline malware protection.
  • Start with one or two ASR rules in audit mode, then expand.
  • Configure BitLocker with USB encryption requirements for data protection.
  • Validate your setup with tools like the EICAR test file.
  • Always pilot before broad deployment to avoid disruptions.

By structuring Endpoint Security policies in Intune, you can achieve a strong balance between security and manageability. Start small, validate thoroughly, and expand as your confidence grows.


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