How to Integrate Microsoft Defender for Endpoint with Intune (and Why You Should)

 Microsoft Defender for Endpoint (MDE) is more than just antivirus — it’s an advanced endpoint protection platform that provides real-time threat detection, response, and automated remediation.

When integrated with Microsoft Intune, you unlock powerful features like:

  • Risk-based Conditional Access
  • Threat-level compliance decisions
  • Visibility into device health and security posture
  • Attack surface reduction at scale

This post walks you through how to integrate Defender for Endpoint with Intune, and how to use that integration to boost your endpoint protection strategy.

1. Why Integrate Defender for Endpoint with Intune?

  • Enforce Conditional Access based on device risk level
  • Mark devices as non-compliant if they have malware or suspicious activity
  • Monitor endpoint security posture directly from Intune
  • Automatically isolate risky endpoints
  • Apply attack surface reduction rules and security baselines centrally

2. Requirements

Before integrating:

  • ✅ Microsoft Defender for Endpoint Plan 1 or Plan 2
  • ✅ Intune license (M365 Business Premium, E3/E5, EMS)
  • ✅ Supported OS: Windows 10/11, iOS/iPadOS, Android, macOS
  • ✅ Devices must be enrolled in Intune
  • ✅ Devices must be joined to Entra ID (Azure AD)

3. Integration Steps (Windows Devices)

Step 1: Enable Endpoint Detection in Intune

  • Go to: intune.microsoft.com (Make sure you've the right permissions)
  • Navigate to Endpoint security > Microsoft Defender for Endpoint
  • Click Open the Microsoft Defender for Endpoint settings
  • Toggle on “Allow Microsoft Defender for Endpoint to enforce Endpoint Security Configurations”
  • Save the settings and it migth take 1-2 hrs for the Connection status to be reflected.
  • Once the connection status is active, under Compliance policy evaluation toggle on "Connect Windows devices version 10.0.15063 and above to Microsoft Defender for Endpoint"
  • You can turn on protection for other devices as well on this screen.

Article content
Article content

Step 2: Enable Integration in Defender Portal

Article content

Step 3: Assign Defender Configuration Profile

  • In Intune, go to Endpoint security > Antivirus
  • Create a policy using Microsoft Defender Antivirus profile
  • Assign to Windows 10/11 device group

Article content

Step 4: Create Compliance Policy Based on Threat Level

  • Go to Devices > Compliance Policies > Create Policy
  • Select platform: Windows 10/11
  • Under Microsoft Defender for Endpoint, choose:

Article content
Article content

Step 5: Set Up Conditional Access in Entra

  • Go to: https://entra.microsoft.com
  • Navigate to Protection > Conditional Access > New Policy
  • Target users/apps
  • Under Grant access, choose:
  • Now, any device that exceeds your risk threshold will be blocked from accessing company resources.

Article content

4. For Mobile Devices (iOS/Android)

  • Use App protection policies + Conditional Access
  • Defender must be installed from the app store and signed in
  • Devices report threat signals to Intune, which then evaluates compliance

5. Monitoring and Reporting

  • Use Endpoint Security > Antivirus dashboard in Intune
  • Review alerts and incidents in Microsoft 365 Defender portal
  • Monitor Device Risk Level in Intune

Article content

6. Pro Tips

  • Always test in a pilot group first
  • Start with “Report-only” mode in Conditional Access
  • Communicate to users why a device might get blocked
  • Use Attack Surface Reduction (ASR) rules with Defender for added protection

Integrating Microsoft Defender for Endpoint with Intune turns your device management into a proactive security engine.

Instead of waiting for incidents, you can block, isolate, and remediate threats in real-time — while giving your team full visibility into endpoint risk.


Comments

Post a Comment

Popular posts from this blog

4 Most common Issues while registering devices with Microsoft Intune MDM

Image
  The built-in Mobile Device Management (MDM) for Office 365 helps you secure and manage your users' mobile devices like iPhones, iPads, Androids, and Windows phones. You can create and manage device security policies, remotely wipe a device, and view detailed device reports. During implementation or deployment, there are some common issues which occur in many of the environment  1-   Windows Update Sometimes you will notice that Windows Update is showing-Up-To-Date but in actual, the version needed for the MDM Registration is not updating automatically and eventually fails every time in the loop Solution Suggested Go to this  link  upgrade your Windows 10 to the latest version You will find a home page like the screenshot below. Click on UPDATE Now button. It will download a .exe file. Run the file and click on UPDATE Now button and press YES. Here it will update your Windows 10 to the Latest Version Note:  You can still work during downloading a...
Read more

Managing Windows Updates with Intune: Best Practices with Update Rings

Image
  Keeping Windows devices up to date is one of the most critical, and often most overlooked, aspects of endpoint security. With Microsoft Intune, you can manage Windows updates centrally using Update Rings , giving you control over when updates install, how users experience restarts, and how you test updates before broad deployment. In this guide, I’ll walk you through: What update rings are Why they’re essential for patch compliance How to configure them in Intune Best practices for rollout and user experience 1. What Are Windows Update Rings in Intune? Update rings in Intune allow you to: Define when and how Windows updates are delivered Set deadlines for installation and restarts Delay feature updates (e.g., to test before production) Control user experience during updates They apply to Windows 10 and 11 devices enrolled in Intune, including those provisioned via Autopilot. 2. Why Update Management Matters Without structured update management, you risk: Devices missing crit...
Read more

The Intune Device Lifecycle: From Onboarding to Retirement (Best Practices)

  Managing endpoints isn’t just about deployment, it’s about handling the entire device lifecycle : from onboarding and day-to-day management to secure deprovisioning when a device is no longer in use. Microsoft Intune provides a streamlined, policy-driven approach to each phase of this lifecycle, and when done right, it reduces IT overhead, increases security, and improves the user experience. In this post, I’ll walk you through the key stages of managing a device in Intune from start to finish, and how to handle each one effectively. Stage 1: Provisioning & Onboarding This is where the device journey begins, and it sets the tone for everything that follows. Tools and features to use: Windows Autopilot for zero-touch setup Enrollment Status Page (ESP) to control setup sequence Dynamic groups to assign configurations automatically Baseline security policies (compliance, Defender, encryption) Goal: Make the first experience smooth, secure, and consistent for every user. Sta...
Read more