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How to Avoid Security Gaps When Switching from MDE Policy Management to Intune

How to Avoid Security Gaps When Switching from MDE Policy Management to Intune

Written By Anoop C Nair
Last Updated February 4, 2026
Posted In Intune
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Key Takeaways:

  • Transition Risks of Moving from Microsoft Defender for Endpoint
  • Security baselines and endpoint protection policies in Intune
  • Intune provides centralized management for compliance
  • Audit existing MDE policies before migration

Let’s discuss How to Avoid Security Gaps When Switching from MDE Policy Management to Intune. Many of the users doubting about when started applying security policies for Defender for Endpoint using MDE to manage them, adding the MDE tag to my Windows 11 machines. And migrating to Intune management, is it necessary to offboard the devices first, before applying the auto-enroll GPO and onboarding device configuration to the machines.

Table of Contents

How to Avoid Security Gaps When Switching from MDE Policy Management to Intune

Migrating from “Security Management for MDE” (where MDE manages the policies) to full Intune management is designed to be a side-by-side transition. Security gap will create if you Offboarding device where the device is unprotected and invisible to your security team during the transition.

Transitioning from MDE Policy Management to Intune

The Transitioning from MDE Policy Management to Intune can be donw with different methods which are recommended by Microsoft. The follow table shows these different methods.

Different Methods
Do Not Run Both Policy Engines at Once
Use Intune Security Baselines
Compliance Integration with Defender
Operational Safeguards
Licensing & Prerequisites
How to Avoid Security Gaps When Switching from MDE Policy Management to Intune – Table.1

Do Not Run Both Policy Engines at Once

Microsoft did not recommended to overlap MDE policy management with Intune. Because it create conflicts and leave gaps in enforcement. Devices should be offboarded from MDE policy management before onboarding into Intune.

Patch My PC

Use Intune Security Baselines

Microsoft recommends adopting Intune’s built-in security baselines (Windows, Edge, Microsoft 365 Apps). These baselines are aligned with CIS benchmarks and provide a consistent starting point for secure configuration.

How to Avoid Security Gaps When Switching from MDE Policy Management to Intune - Fig.1
How to Avoid Security Gaps When Switching from MDE Policy Management to Intune – Fig.1

Compliance Integration with Defender

Intune compliance policies should reference Defender for Endpoint’s machine risk score. Ensure risk score sync between Intune and Defender is monitored to avoid false compliance failures.

How to Avoid Security Gaps When Switching from MDE Policy Management to Intune - Fig.2
How to Avoid Security Gaps When Switching from MDE Policy Management to Intune – Fig.2

Operational Safeguards

Microsoft recommends using the Intune portal + Microsoft 365 Defender portal for unified visibility of Application Control and compliance events.

Licensing & Prerequisites

Ensure devices are licensed with Microsoft 365 E5 (or equivalent) for full Defender + Intune integration. And Devices must be Entra ID joined, Defender onboarding package applied, Intune enrollment completed before migration.

How to Avoid Security Gaps When Switching from MDE Policy Management to Intune - Fig.3 - Creds to MS
How to Avoid Security Gaps When Switching from MDE Policy Management to Intune – Fig.3 – Creds to MS

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Author

Anoop C Nair has been Microsoft MVP for 10 consecutive years from 2015 onwards. He is a Workplace Solution Architect with more than 22+ years of experience in Workplace technologies. He is a Blogger, Speaker, and Local User Group Community leader. His primary focus is on Device Management technologies like SCCM and Intune. He writes about technologies like Intune, SCCM,  Windows,  Cloud PC,  Windows, Entra, Microsoft Security, Career, etc.

Written by

Anoop C Nair is Workplace Technology solution architect with 25+ years of experience in global enterprise organizations such as JP Morgan, Capgemini, etc. Microsoft Certified Trainer. Microsoft MVP from 2015 onwards for consecutive 11+ years! He also conducts Intune and modern workplace tech training for enterprise organizations. He is Blogger, Speaker, and Founder of HTMD Community and HTMD Conference. His main focus is on Device Management technologies like Intune, Windows, Cloud PC. He writes about technologies like Intune, SCCM, Windows, Cloud PC, Windows, Entra, Microsoft Security.

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