Endpoint management has long since moved beyond just laptops and desktops to include servers, mobile devices, virtual desktops, and point-of-sale (POS) systems. With Intune and SCCM/MECM, Microsoft offers two solutions that serve as the core of endpoint management for many companies—each with different approaches, strengths, and use cases.
The relevance of both UEM solutions is highlighted in our study, "State of Endpoint Management in DACH 2025/26": 76 percent of the companies surveyed use at least one of the two tools.
In this article, we compare Intune and SCCM/MECM, outline typical use cases, and explain when co-management or a phased migration makes sense.
Key takeaways
- Intune is a cloud-based UEM solution for the modern management and security of Windows, macOS, Android, and iOS devices.
- SCCM/MECM is an on-premises solution offering deep control—ideal for complex local infrastructures and regulated environments.
- Key differences: Intune is cloud-based, cross-platform, integrated into M365, and offers modern security features like Conditional Access. SCCM is local, Windows-centric, and provides highly granular control.
- Recommendation: Intune is the standard for modern client management. SCCM is suitable for highly available or complex on-prem infrastructures. Co-management allows you to use both solutions in combination.
How SOFTTAILOR supports you: We analyze your environment, optimize existing Intune or SCCM setups, or develop a robust endpoint management strategy that aligns perfectly with your goals.
1. What is Microsoft Intune?
Microsoft Intune is a cloud-based Unified Endpoint Management (UEM) solution that enables centralized management of PCs, mobile devices, and specialized systems—regardless of location or operating system. It supports Windows, macOS, iOS/iPadOS, Android, and, to some extent, Linux.
As part of the Microsoft ecosystem, Intune integrates seamlessly with Microsoft 365, Entra ID (Azure AD), and Defender for Endpoint. The platform combines Mobile Device Management (MDM) and Mobile Application Management (MAM), allowing both devices and individual applications to be managed securely — even in BYOD scenarios.
Intune supports automated provisioning (zero-touch deployment) with Windows Autopilot, offers cloud-based policy and app management, and provides transparent insights into device health and user experience via Endpoint Analytics. This makes Intune a core component for modern, secure, and scalable endpoint management.
2. What is SCCM / MECM?
The Microsoft Endpoint Configuration Manager – formerly known as SCCM (System Center Configuration Manager) – is an on-premises solution for managing Windows devices in corporate networks. The platform enables comprehensive control over software distribution, operating system deployment, patch management, inventory, and security policies.
Unlike Intune, SCCM relies on local infrastructure with its own servers and databases. This allows systems to be deeply integrated into existing IT landscapes and configured very specifically – albeit with a higher administrative overhead. SCCM offers clear advantages, especially in regulated environments or for complex deployment scenarios.
SCCM/MECM continues to demonstrate its strengths in complex deployment scenarios as well. In addition to multi-stage software installations via task sequences, the solution also supports full operating system deployments and bare-metal deployments.
3. Intune vs. SCCM/MECM – The key differences
Both UEM solutions take different approaches to managing your devices. Which solution best suits your company's requirements depends on your infrastructure, your security needs, and your IT operating model.
With the annual release cadence of SCCM , it is becoming clear where Microsoft is heading in the long term: new features are primarily being developed for Intune, while SCCM/MECM focuses on stability and security. Nevertheless, Intune cannot yet replace SCCM/MECM in all areas of application. A detailed comparison is therefore still worthwhile:
Licensing & Costs
Intune is included in Microsoft 365 E3 and E5, among others. Most Intune licenses include concurrent usage rights for SCCM/MECM for managing licensed clients. Separate licensing requirements apply to the management of Windows Servers. In addition, there are the costs for setting up, operating, and maintaining the local SCCM infrastructure.
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On-Premises vs. Cloud
In many tool comparisons, on-premises vs. cloud is a key decision criterion. Intune is entirely cloud-based and requires no server infrastructure of its own. Device management can be performed from any location. In contrast, SCCM is operated locally and is particularly well-suited for environments with a centralized network architecture or specific compliance requirements.
Usability
Intune scores points with a modern user interface and ease of use – even for IT teams without in-depth prior knowledge. SCCM is more complex to set up and administer, but it offers greater granularity and control in return.
Security and Compliance
Both systems can be combined with Microsoft security solutions such as Defender for Endpoint . Intune offers additional benefits through native integration with Microsoft Entra ID, Conditional Access and automated compliance policies.
Integration with Microsoft 365
Intune is deeply integrated into Microsoft 365 . Features such as app protection policies, single sign-on, and endpoint analytics are available to you right out of the box. While SCCM can be integrated, it requires additional configuration effort.
Pros and cons at a glance
4. Using them together: Intune and SCCM in co-management
Intune and SCCM/MECM do not necessarily have to be viewed separately. With co-management , Windows devices can be managed in parallel via both platforms, and individual workloads can be gradually migrated to Intune.
This allows you to leverage modern cloud features while your existing deployment, software distribution, or management processes remain in SCCM/MECM for the time being. Companies benefit from a flexible transition phase that protects existing investments while simultaneously introducing new capabilities. Furthermore, this approach reduces migration risks by ensuring that changes are implemented in a controlled, step-by-step manner.
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5. Conclusion: Intune, SCCM, or both?
The right strategy for Unified Endpoint Management depends primarily on your existing systems, the types of devices being managed, and your specific deployment requirements. For companies that are already heavily cloud-based or are planning to move in that direction, Intune offers a modern, flexible, and low-maintenance solution with tight integration into Microsoft 365.
SCCM/MECM remains relevant, particularly for complex on-premises infrastructures, specific compliance requirements, and custom deployment scenarios. Larger organizations with specialized IT teams, multiple locations, and extensive Windows environments also benefit from its high level of granular control.
Our tip: Get the best of both worlds. With the co-management model, you can introduce new cloud features step-by-step without discarding processes that are already working well. This keeps you flexible—and ready for the future. You can find support for strategy, implementation, or optimization in our Intune and SCCM Consulting.
Dorian has been involved in corporate and IT strategy since 2011. Due to the endpoint security deficiencies of many companies and the information overload, he developed the endpoint strategy. Dorian is co-founder of the “Endpoint Management” expert group at IAMCP e.V.
Years of Experience
Managed Endpoints
