Troubleshooting Microsoft Intune Issues A Practical Guide for IT Admins

Microsoft Intune is a powerful platform for managing devices, apps, and security policies across your enterprise. But like any complex service, it can present challenges. Whether you’re dealing with device enrollment failures, policy misapplications, or app deployment issues, effective troubleshooting is critical to maintaining a smooth user experience and secure environment.

In this post, I’ll walk through practical steps and tools to troubleshoot common Intune issues, with insights drawn from real-world scenarios.

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🛠 Common Categories of Intune Issues

Before diving into troubleshooting, it’s helpful to classify the types of issues you might encounter:

• Device Enrollment Failures
• Configuration Profile Not Applying
• App Deployment Failures
• Compliance Policy Issues
• Conditional Access Problems
• Reporting and Sync Delays

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🔍 Step-by-Step Troubleshooting Approach

1. Verify Service Health First

Always begin by checking the Microsoft 365 Service Health Dashboard. If Intune is experiencing service-wide issues, that might be your culprit.

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2. Review Device Sync and Enrollment Logs

For Windows devices, key places to look include:

• Event Viewer → Applications and Services Logs → Microsoft → Windows → DeviceManagement-Enterprise-Diagnostics-Provider
• MDMDiagReport.xml (generated via mdmdiagnosticstool.exe -area DeviceEnrollment;DeviceProvisioning -cab c:\temp)

On iOS/Android: Use the Company Portal app’s diagnostics option to export logs.

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3. Check Intune Management Extension (IME)

IME is responsible for executing PowerShell scripts and Win32 apps on Windows 10/11 devices.

• Verify it’s installed: C:\Program Files (x86)\Microsoft Intune Management Extension
• Logs are located here: C:\ProgramData\Microsoft\IntuneManagementExtension\Logs
• Common log files:
  • IntuneManagementExtension.log – script and app install statuses
  • AgentExecutor.log – script execution details

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4. Use the Troubleshooting Blade in Intune Admin Center

Navigate to Devices > Troubleshoot in the Intune portal. You can search by user and view a breakdown of device compliance, config profiles, app install status, and more.

This is especially useful to identify:

• Which policies failed
• Reasons for non-compliance
• Pending vs succeeded configurations

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5. Verify Group Assignments

Many issues stem from incorrect Azure AD group assignments:

• Is the device/user in the targeted group?
• Is the group dynamic? If so, check membership rules.
• Use Azure AD portal to simulate the group membership for a user/device.

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6. Confirm Configuration and Compliance Profile Status

Go to:

• Devices > Configuration Profiles > [Profile] > Device status
• Devices > Compliance policies > [Policy] > Report

Make sure there are no conflicts, assignments are accurate, and target platforms match the device OS.

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7. App Deployment Diagnostics

For Win32 apps:

• Check IntuneManagementExtension.log and AgentExecutor.log
• Ensure app dependencies are met
• Validate detection rules

For Store/iOS/Android apps:

• Review installation status under Apps > Monitor > App install status
• Make sure the app is assigned as Required for automatic deployment

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🧪 Advanced Tools and Techniques

• Graph API: Query device and policy status for automation and diagnostics
• Endpoint Analytics: Get performance insights and proactive recommendations
• Log Analytics (if integrated with Defender or Log workspace): For deeper telemetry

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✅ Pro Tips for Efficient Troubleshooting

• Document every policy and group assignment
• Establish a test group and device for new configurations
• Use naming conventions for policies (e.g., WIN_Config_Baseline_Policy)
• Use Scope Tags to control admin visibility and reduce misconfiguration

Intune is deeply integrated with Azure AD, Microsoft Defender, and Microsoft 365, making troubleshooting occasionally complex but also deeply insightful. Having a structured approach, combined with the right logging and diagnostic tools, can dramatically reduce your resolution time.

If you’re frequently managing a complex environment, consider using automation scripts (via Graph API or PowerShell SDK) to audit policy compliance and device health regularly.