A Complete Guide to SCCM to Intune Migration

 

Introduction

As organizations continue to modernize their IT infrastructure, migrating from traditional on-premises solutions like System Center Configuration Manager (SCCM) to cloud-native platforms such as Microsoft Intune has become a strategic priority. Intune, part of Microsoft Endpoint Manager (MEM), provides modern management capabilities, streamlined deployment, and robust security—ideal for hybrid and remote workforces.

This article provides a step-by-step guide to help IT admins plan and execute a successful SCCM to Intune migration.

Why Migrate from SCCM to Intune?

Feature SCCM Intune Infrastructure On-prem Cloud-based OS Deployment Traditional imaging Autopilot & provisioning packages App Deployment MSI, EXE MSI, EXE, Win32, LOB, Store apps Device Management Primarily Windows Windows, macOS, iOS, Android Updates WSUS/Manual Cloud-integrated, with Windows Update for Business Cost Requires infrastructure Reduces infra/maintenance cost

Pre-Migration Considerations

  1. Assess Your Environment
  2. Licensing Requirements Ensure you have:
  3. Device Enrollment Strategy Plan how devices will be enrolled into Intune:

Step-by-Step Migration Approach

Phase 1: Enable Co-Management

Co-management allows you to manage Windows devices with both SCCM and Intune simultaneously.

Steps:

  1. In SCCM console, go to Administration > Cloud Services > Co-management.
  2. Select Configure Co-management.
  3. Sign in with your Azure AD account.
  4. Choose workloads to switch (start with Pilot group).
  5. Configure auto-enrollment to Intune.

🔍 Tip: Start with workloads like Compliance Policies and Resource Access.

Phase 2: Evaluate Workload Transition

Begin moving workloads from SCCM to Intune. Suggested order:

  1. Compliance Policies
  2. Device Configuration
  3. Windows Updates
  4. Endpoint Protection
  5. App Deployment

Use Pilot groups before global rollout.

Phase 3: Modernize OS Deployment (Autopilot)

Instead of traditional SCCM imaging, switch to Windows Autopilot for provisioning new devices.

Setup:

  1. Capture hardware hashes.
  2. Upload to Intune via Devices > Windows > Windows enrollment > Devices.
  3. Create Autopilot deployment profile.
  4. Assign to dynamic groups based on device attributes.

🚀 Benefit: Zero-touch provisioning for remote users.

Phase 4: Application Migration

Repackage apps from SCCM and deploy via Intune:

App Type SCCM Intune Equivalent MSI MSI MSI (LOB app) EXE Package Win32 app (using IntuneWin tool) Scripts Task sequences PowerShell scripts via Intune

Use the Microsoft Win32 Content Prep Tool to package .intunewin files.

Phase 5: Migrate Configuration Baselines

Migrate Group Policies and Configuration Baselines to Intune:

  1. Use Group Policy Analytics in Intune to evaluate existing GPOs.
  2. Convert supported GPOs to Configuration Profiles.
  3. Apply profiles and monitor compliance.

🛠️ Use Policy CSPs and OMA-URI for custom configurations.

Phase 6: Retire SCCM Clients

Once all workloads are moved:

  1. Remove SCCM client using script or uninstall via Intune.
  2. Decommission Distribution Points and Management Points.
  3. Keep SCCM around for reporting or legacy device support (optional).

Monitoring and Reporting

Use:

  • Intune Admin Center for device compliance, enrollment status, and app deployment
  • Log analytics integration for custom reports
  • Endpoint analytics for performance and user experience tracking

Challenges and Best Practices

🔧 Common Challenges

  • Legacy app compatibility
  • Intune Win32 packaging complexity
  • Network bandwidth during migration
  • User training and communication

✅ Best Practices

  • Start with pilot users/groups
  • Use phased approach with rollback options
  • Automate as much as possible (PowerShell, Proactive Remediations)
  • Document all configurations
  • Continuously monitor and optimize

Conclusion

Migrating from SCCM to Intune is not a simple lift-and-shift but a transformation in how devices are managed. With the right planning, phased rollout, and stakeholder alignment, organizations can benefit from a more flexible, secure, and cloud-centric device management strategy.

Whether you’re planning to fully replace SCCM or operate in co-managed mode for the long term, this guide can serve as your roadmap to a successful migration.

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