Best Practices for Co-Management Workload Distribution in SCCM and Intune
As IT environments evolve, many organizations are moving from traditional, on-premises management to a more cloud-connected approach.
This transition brings up one of the most common questions for administrators:
How should workloads be distributed between SCCM (Configuration Manager) and Intune in a co-managed setup?
Over the years, SCCM has proven itself as a powerhouse for managing Windows Servers and complex enterprise environments, offering deep visibility and control.
On the other hand, Intune introduces a modern, cloud-first model, bringing agility, remote capability, and tighter integration with Azure AD and security features.
The key is finding the right balance deciding which workloads should stay under SCCM’s robust on-prem management, and which ones can be confidently moved to Intune for a more flexible, modern experience.
Understanding Co-Management Workloads
Co-management allows both SCCM and Intune to manage the same Windows 10/11 device. Workloads define which system has authority over a specific management area.
| Workload | Description |
|---|---|
| Compliance Policies | Evaluates device compliance and triggers conditional access decisions. |
| Resource Access Policies | Manages VPN, Wi-Fi, and email profiles. |
| Windows Update Policies | Controls Windows Update for Business and patching rules. |
| Endpoint Protection | Manages Defender AV and security baselines. |
| Device Configuration | Applies configuration profiles and security settings. |
| Application Deployment | Handles app deployment and lifecycle management. |
| Office Click-to-Run | Deploys and manages Microsoft 365 Apps. |
General Best Practices Before You Start
Move gradually – Don’t flip everything at once. Start with low-impact workloads like Compliance Policies.
Use pilot collections – Always test changes with a small, controlled group before full rollout.
Assess cloud readiness – Intune works best when devices are hybrid or Azure AD joined.
Keep visibility unified – Use SCCM and Intune reports together to maintain a single view.
Have a rollback plan – In case of policy conflicts or unforeseen behavior, you’ll need an easy way back.
Workload-by-Workload Recommendations
1. Compliance Policies
Recommended Owner: Intune
Why:
Compliance policies integrate directly with Azure AD Conditional Access, allowing real-time access control for hybrid and cloud environments.
Pros:
- Real-time compliance checks in the cloud
- Direct Conditional Access integration
- Simplifies hybrid identity scenarios
Cons:
- Requires stable internet connectivity
- Offline compliance checks are limited
Best Practice:
Start with this workload. It’s the easiest to transition and delivers immediate value in security and access control.
2. Resource Access Policies (VPN, Wi-Fi, Email)
Recommended Owner: Depends on your infrastructure
Why:
If your users still rely heavily on on-premises services like Exchange or internal VPN, SCCM offers better reliability.
For cloud-native or hybrid environments using Exchange Online, Intune simplifies deployment and targeting.
Pros (Intune):
- Easy integration with Azure AD groups
- Simplified setup for remote or hybrid workers
Pros (SCCM):
- Reliable for on-prem AD environments
- Works without continuous internet access
Best Practice:
Keep it in SCCM until your key network and mail services are fully cloud-based.
3. Windows Update Policies
Recommended Owner: Start with SCCM → Move gradually to Intune
Why:
SCCM offers precise update control through WSUS and ADRs, while Intune’s Windows Update for Business (WUfB) simplifies delivery with less infrastructure.
Pros (Intune):
- No WSUS or DPs needed
- Flexible deferral policies
- Easier for remote endpoints
Pros (SCCM):
- Advanced compliance reporting
- Full visibility into patch status
- Bandwidth and timing control
Best Practice:
Keep patching in SCCM until you have confidence in WUfB reporting and compliance visibility.
4. Endpoint Protection
Recommended Owner: Intune
Why:
Defender for Endpoint integrates tightly with Intune and the Microsoft 365 Defender portal, enabling advanced protection scenarios.
Pros:
- Unified security dashboard
- Easy ASR and baseline deployment
- Centralized cloud-based visibility
Cons:
- Some advanced Defender settings still managed better in SCCM
Best Practice:
Migrate once all endpoints are onboarded to Microsoft Defender for Endpoint and reporting is validated.
5. Device Configuration
Recommended Owner: Intune
Why:
Modern configuration management through Intune is faster, scalable, and cloud-aware.
It’s ideal for enforcing policies like BitLocker, password rules, or hardening profiles.
Pros:
- Real-time policy evaluation
- Built-in compliance integration
- Supports hybrid and AAD-joined devices
Cons:
- Reporting isn’t as detailed as SCCM baselines
- GPO parity still requires custom CSPs
Best Practice:
Use Intune Security Baselines for new devices. Keep SCCM baselines for legacy or isolated systems.
6. Application Deployment
Recommended Owner: Hybrid (SCCM + Intune)
Why:
SCCM remains superior for large and complex application packages, especially those with dependencies or sequencing.
Intune shines for lightweight apps, Microsoft 365 components, and remote users.
Pros (SCCM):
- Detailed deployment tracking
- Dependency and supersedence control
- Bandwidth management (DPs, Peer Cache)
Pros (Intune):
- Cloud delivery, no infra needed
- Simple for remote workers
- Company Portal integration
Best Practice:
Keep business-critical and large apps in SCCM; move modern or SaaS apps to Intune.
7. Office Click-to-Run
Recommended Owner: Intune
Why:
Deploying Microsoft 365 Apps through Intune is straightforward, policy-driven, and designed for cloud environments.
Best Practice:
Use Intune for M365 Apps; fallback to SCCM only when offline or restricted deployments are required.
Summary: Recommended Workload Distribution
| Workload | Recommended Owner | Transition Priority |
|---|---|---|
| Compliance Policies | Intune | High |
| Resource Access | Depends | Medium |
| Windows Updates | Hybrid → Intune | Medium |
| Endpoint Protection | Intune | High |
| Device Configuration | Intune | High |
| Application Deployment | Hybrid | Medium |
| Office Click-to-Run | Intune | High |
Final Thoughts
Finding the right workload balance between SCCM and Intune isn’t just about ticking boxes, it’s about aligning your management approach with your organization’s goals.
For endpoints, moving workloads to Intune enables modern capabilities like Conditional Access, automated compliance, and simplified deployment ,all without maintaining on-prem infrastructure.
It’s a forward-looking, scalable way to manage devices in a hybrid world.
But when it comes to Windows Server, SCCM still holds the crown.
Its control, visibility, and reliability remain unmatched, especially for patching, compliance, and configuration in enterprise environments.
In short:
- Intune leads the future of endpoint management.
- SCCM remains the trusted backbone for servers and enterprise control.
