What is SCCM & Intune?

System Center Configuration Manager (SCCM), or Microsoft Configuration Manager, is an endpoint management solution useful for on-premises environments. It manages domain-linked Windows devices and software and OS deployment through local infrastructure like Distribution Points.
Microsoft Intune is a cloud-based endpoint management solution. It comes with the Microsoft 365 suite. It integrates Unified Endpoint Management (UEM) with Mobile Device Management (MDM) across Windows, macOS, iOS, and Android devices. Intune also enables IT teams to handle remote and hybrid mobile devices from a centralized location. This doesn’t require VPNs or local network connectivity.

The primary difference between the two platforms is the management system. SCCM is suitable for traditional infrastructure, while Intune suits advanced, cloud-based endpoint control. Many enterprises therefore use co-management for migrating from SCCM to intune.

What is Co-Management and Why It is the Recommended Migration Strategy 

SCCM co-management Intune refers to the process where SCCM and Intune are used to manage devices together as the workloads are migrated in phases.  

This minimizes disruption, reduces risk, and allows IT teams to validate each workload before retiring their on-premises infrastructure. Migrating directly from SCCM to Intune can create unnecessary risk. Your existing application deployments, software updates, and security policies often have years of customizations behind them. So this makes this expensive and time-consuming. 

 So, why do we recommend this? Well, with the co-management approach, you can: 

• Continue managing existing devices through SCCM 
• Introduce Intune policies gradually 
•  Test cloud management with pilot users 
• Roll back workloads if issues arise 
• Migrate remote users without relying on VPN connection 

SCCM to Intune Migration – A Step-by-step Guide

Let us now dive into the process that we follow here at Evolvous when it comes to moving endpoint management and other workloads from Microsoft Configuration manager to Microsoft Intune.

Step 1: Assess Your Existing SCCM Environment 

Before enabling Intune, we need to perform a complete inventory of your SCCM environment. This assessment determines what should be migrated, modernized, or retired. 

In most cases, we will document: 

• Device collections and boundaries 
• Applications and deployment packages 
• Task sequences 
• Software update groups and Automatic Deployment Rules (ADRs) 
• Configuration Baselines 
• Group Policy dependencies 
• Operating system images 
• Client health status 
• Distribution Points and Site Servers 

This is also the time when we remove unused applications, duplicate collections, and outdated deployment packages that no longer provide value to your organization. 

Step 2: Prepare Your Microsoft Intune Environment 

 Now, we work towards building the new Intune environment. A successful migration starts with a properly configured cloud environment. 

We normally begin by validating your identity infrastructure: 

• Microsoft Entra ID synchronization 
• Hybrid or Entra ID Join 
• Multi-Factor Authentication 
• Device registration 

Next, we will configure Intune by creating: 

• Device groups 
• Role-Based Access Control (RBAC) 
• Enrollment policies 
• Compliance policies 
• Configuration profiles 
• Endpoint Security policies 
• Company Portal branding 

Together with you, we will define naming standards and administrative boundaries before enrolling the production devices. Consistent governance at this stage simplifies long-term management. 

Step 3: Enable Co-Management 

Once both environments are ready, we will enable co-management from the Configuration Manager console. 

During this stage, our team will: 

• Connect SCCM to your Microsoft tenant using Cloud Attach
• Configure the Cloud Management Gateway (CMG) if internet-based management is required
• Enable automatic Intune enrollment for supported Windows devices
• Create pilot device collections instead of migrating every endpoint immediately

We always prefer to start with a small pilot group before expanding to additional departments. 

Step 4: Migrate Management Workloads Gradually 

At Evolvous, we believe that migration is not only about moving devices. It is about moving workloads as well. 

A common migration sequence is:

1. Compliance Policies: Recreate compliance rules in Intune and validate reporting. 
2. Device Configuration: Replace Configuration Baselines and GPO settings with Intune Configuration Profiles. 
3. Endpoint Protection: Move Microsoft Defender policies to Intune Endpoint Security. 
4. Resource Access: Configure Wi-Fi, VPN, certificates, and email profiles. 
5. Windows Updates: Replace WSUS policies with Windows Update for Business deployment rings. 
6. Client Applications: Deploy applications through Intune using Win32 packages. 

After we have migrated each workload, we will monitor policy deployment, compliance status, and user experience before moving the next workload. 

Step 5: Repackage and Modernize Applications 

Application migration is often the longest phase of the project. Many SCCM deployments use legacy installation methods that require modernization before they can be deployed through Intune. We review the applications to determine whether they should be: 

• Converted into Win32 packages 
• Delivered through the Microsoft Store 
• Installed using PowerShell scripts 
• Replaced with newer cloud-native versions 
• Retired completely  

Step 6: Replace Group Policies with Intune Policies 

Your organizations might rely heavily on Active Directory Group Policy. Rather than recreating every policy manually, we use Group Policy Analytics to identify settings that can be migrated directly into Intune. 

Here are some of the settings that we commonly migrate:

• Password requirements 
• BitLocker encryption 
• Microsoft Defender settings 
• Firewall configuration 
• Browser security 
• USB device restrictions 
• Windows security baselines 

Step 7: Modernize Windows Updates and Device Provisioning 

One of the biggest advantages of Intune is cloud-native update management. 

 Instead of maintaining WSUS infrastructure, most of our clients move to: 

• Windows Update for Business 
• Feature Update policies 
•  Quality Update rings 
• Delivery Optimization 
• Windows Autopatch 

Step 8: Validate Before Expanding 

Now, we are at the end of the migration process. Every migration phase should end with validation. 

At this stage, we will monitor key metrics such as: 

• Device enrollment success 
• Policy deployment success 
•  Application installation rates 
• Update compliance 
• BitLocker compliance 
• Microsoft Defender onboarding 
• User support tickets 

Once the test users demonstrate stable performance, we will expand deployment in phases by department, location, or business unit. So, why do we do this? This phased rollout minimizes operational risk and makes troubleshooting significantly easier. 

Step 9: Decommission SCCM 

We will decommission SCCM only after all workloads have successfully transitioned to Intune. The decommissioning process includes: 

• Removing Distribution Points 
• Retiring Management Points 
• Removing Software Update Points 
• Decommissioning WSUS integration 
• Cleaning up boundary groups 
• Removing obsolete collections 
• Uninstalling Configuration Manager clients where appropriate 
• Archiving reports and documentation 

Also Read: Jamf to Intune Migration Guide

Enterprise Checklist for Migrating from SCCM to Intune

Moving from SCCM to Intune is not just changing your security platform. Before you move your endpoint control to the cloud, take these crucial measures:

• Evaluate Existing Setup: Review your current SCCM workloads, working apps, Group Policies (GPOs), and workflow pattern. This helps you decide what to relocate or quit.
• Identity & Licensing Structure: Confirm Microsoft Entra ID (Azure AD) links, create Hybrid Entra Join, and allocate proper Microsoft 365 / Intune licenses.
• Allow Co-Management: Link SCCM to cloud benefits via Cloud Attach. This helps you control endpoints concurrently during the shift.
• Repurpose Applications: Turn legacy desktop software packages into Win32 app format (.intunewin). This provides a flawless cloud deployment.
• Establish Rules: Redesign compliance policies, security structure, and Windows Update for Business guidelines inside Intune.
• Trial with a small batch: Verify rules, applications, security management, and user feedback before you totally migrate from SSCM to Intune.
• Create a rollback strategy: Set a recovery rule to apply if any issue occurs at any stage of the deployment.
• Review after migration: Monitor device compliance, application settings, policy frictions, and user experiences.

Need Help Migrating Your Workloads to Intune?

Migrating compliance policies, device configurations, Defender settings, Windows Updates, and applications is a significant undertaking.

Our certified Microsoft Intune consultants handle every workload transition — so your IT team can focus on the business.

What are Some Common Migration Challenges that You Might Face?

Microsoft Configuration manager to Intune migration is not free from challenges. Here are some of the common challenges that you might face and how we can help you fix them: 

Challenge	How We Fix It
Devices fail to enroll in Intune	We validate Microsoft Entra registration and enrollment policies.
Applications fail after migration	Our team usually repackages them as Win32 apps and review detection rules.
Policy conflicts occur	Remove overlapping Group Policy settings before enabling Intune equivalents.
Remote users cannot receive updates	Deploy Cloud Management Gateway and Windows Update for Business.
Migration takes longer than expected	Prioritize business-critical workloads and migrate in phases rather than all at once.

How Does Evolvous Help with SCCM to Intune Migration?

Migrating endpoint management platforms is more than a technical upgrade. At Evolvous, we treat it is an opportunity to modernize security, simplify device management, and prepare for a cloud-first workplace. 

Our Intune migration consultants will begin every migration with a detailed SCCM health assessment, followed by Intune readiness planning, application modernization, co-management configuration, policy migration, Windows Autopilot deployment, and phased production rollout. Every migration is designed to minimize downtime while maintaining compliance, security, and business continuity. 

Whether you are managing 200 devices or 20,000, our phased migration methodology helps reduce deployment risk while ensuring users experience a seamless transition to cloud-based endpoint management. 

Get a Quote for SCCM to Intune Migration

Contact Our team today to get a FREE Quote for SCCM to Intune Migration and discover how you can boost the endpoint security across your workspace.

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Frequently Asked Questions 

1. Can SCCM and Intune manage the same device?

Yes. Co-management allows both platforms to manage a device simultaneously while workloads are transitioned gradually. 

2. How long does an SCCM to Intune migration take?

Most organizations complete the migration in 6–16 weeks, depending on the number of devices, applications, and existing infrastructure. 

3. Do all applications need to be rebuilt?

No. Many applications can be migrated directly, while older packages may require repackaging as Win32 applications or modernization. 

4. Can remote users migrate without a VPN?

Yes. When Cloud Management Gateway, Microsoft Entra ID, and Intune enrollment are configured correctly, remote devices can be managed securely over the internet. 

5. When should SCCM be retired?

Only after all management workloads, applications, updates, and security policies have been validated in Intune and production, users have successfully transitioned.