Microsoft offers two primary endpoint management platforms: Microsoft Intune (cloud-native) and Microsoft Endpoint Configuration Manager (SCCM/ConfigMgr, on-premises). Both manage devices, deploy applications, enforce compliance, and distribute updates—but they take fundamentally different architectural approaches.
With Microsoft investing heavily in Intune and positioning it as the future of endpoint management, many organizations face a critical decision: migrate to Intune, stay with SCCM, or run both through co-management. This guide breaks down the differences, compares capabilities, and provides a practical framework for choosing the right path.
What Is Microsoft Intune?
Microsoft Intune is a cloud-native endpoint management platform that is part of the Microsoft Intune product family (formerly Microsoft Endpoint Manager). It manages devices and applications through the cloud without requiring on-premises infrastructure.
Intune manages devices using Mobile Device Management (MDM) and Mobile Application Management (MAM) protocols. Devices enroll in Intune and receive policies, configurations, and applications directly from the cloud service.
Key characteristics:
- Cloud-only architecture—no on-premises servers required
- Manages Windows, macOS, iOS, Android, and Linux devices
- Integrates natively with Microsoft Entra ID (Azure AD) and Microsoft 365
- Supports both corporate-owned and BYOD devices
- Accessed through the Microsoft Intune admin center (web-based console)
What Is SCCM (Configuration Manager)?
System Center Configuration Manager (SCCM), now officially named Microsoft Endpoint Configuration Manager (ConfigMgr), is an on-premises endpoint management platform that has been the enterprise standard for Windows management for over two decades.
SCCM manages devices using a client-agent model. The Configuration Manager client is installed on each managed device and communicates with on-premises site servers, management points, and distribution points.
Key characteristics:
- On-premises architecture requiring site servers, SQL databases, and distribution infrastructure
- Deep Windows management capabilities built over 20+ years
- OS deployment (OSD) with task sequences
- Software metering, asset intelligence, and detailed hardware/software inventory
- Granular patch management with maintenance windows and deployment rings
Intune vs SCCM: Comparison Table
| Capability | Microsoft Intune | SCCM (ConfigMgr) |
|---|---|---|
| Architecture | Cloud-native (SaaS) | On-premises (server infrastructure) |
| Device Enrollment | MDM/MAM enrollment (zero-touch capable) | Client agent installation |
| OS Deployment | Windows Autopilot (cloud-driven) | Task sequences (PXE, media, network) |
| Platform Support | Windows, macOS, iOS, Android, Linux | Windows (primary), macOS (limited), Linux (limited) |
| Patch Management | Windows Update for Business, update rings | WSUS integration, software update groups, maintenance windows |
| App Deployment | Win32 apps, LOB apps, Microsoft Store, web apps | MSI, Script, App-V, task sequence-based, complex dependencies |
| Compliance Policies | Cloud-based conditional access integration | Compliance baselines, configuration items |
| Reporting | Intune reports, Log Analytics integration | Extensive built-in reporting, SQL-based custom reports |
| BYOD Support | Strong — MAM without enrollment | Limited — requires client installation |
| Bandwidth Management | Cloud-optimized (Delivery Optimization, Connected Cache) | Distribution points, BranchCache, peer cache |
| Infrastructure Cost | No on-premises servers | Site servers, SQL Server, distribution points, network infrastructure |
| Licensing | Included in Microsoft 365 E3/E5, EMS E3/E5, or standalone | Requires System Center or Microsoft Intune + ConfigMgr license |
| Internet Management | Native — designed for internet-connected devices | Requires CMG (Cloud Management Gateway) for internet clients |
| Scripting/Automation | Proactive remediations, PowerShell scripts via Intune | Comprehensive scripting, task sequences, PowerShell, compliance scripts |
Architecture Differences
The fundamental difference between Intune and SCCM is their management plane.
Intune: Cloud-Native Management
Intune operates entirely in the cloud. There are no servers to deploy, patch, or maintain. Devices communicate with the Intune service over HTTPS, making them manageable from anywhere with an internet connection.
This architecture is ideal for organizations with:
- Remote and hybrid workforces
- BYOD policies that need mobile device security without domain joining
- Limited IT infrastructure staff
- Multi-platform environments (Windows, Mac, iOS, Android)
The trade-off is that cloud management relies on MDM protocols, which offer less granular control than SCCM’s agent-based approach for certain advanced Windows management scenarios.
SCCM: On-Premises Management
SCCM requires significant on-premises infrastructure: primary site servers, secondary site servers (for large environments), management points, distribution points, SQL Server databases, reporting services points, and potentially a Cloud Management Gateway for internet-connected clients.
This architecture is suited for organizations with:
- Large on-premises device fleets
- Complex OS deployment requirements (bare metal imaging, task sequences)
- Strict data sovereignty requirements
- Advanced software distribution needs with complex dependency chains
- Existing investment in SCCM infrastructure and expertise
Management Capabilities Compared
Device Configuration
Intune uses configuration profiles based on MDM CSPs (Configuration Service Providers) and the Settings Catalog. The Settings Catalog now exposes thousands of settings, closing the gap with Group Policy. Intune also supports ADMX-backed policies, security baselines, and endpoint security profiles.
SCCM uses configuration baselines, compliance settings, and Group Policy through the domain. SCCM’s configuration management has deep legacy support and can manage virtually any Windows setting through scripts, configuration items, and desired configuration management.
Verdict: For modern Windows 10/11 management, Intune’s Settings Catalog covers the majority of configuration needs. SCCM retains advantages for legacy application configurations and highly complex scripted configurations.
Application Deployment
Intune deploys Win32 apps (packaged as .intunewin files), Microsoft Store apps, LOB apps, web apps, and Microsoft 365 Apps. Win32 app deployment supports requirements rules, dependencies, and supersedence. However, Intune’s application deployment lacks the depth of SCCM’s task sequence-based deployments for complex installation scenarios.
SCCM offers the most comprehensive application deployment capabilities in the Microsoft ecosystem. Task sequences can chain multiple installations with reboots, configure applications post-install, handle complex dependencies, and manage application retirement. SCCM also supports App-V virtualization and detailed software metering.
Verdict: SCCM remains superior for complex application deployment scenarios. Intune handles standard application deployment effectively and continues to add capabilities with each service update.
Patch Management
Intune manages Windows updates through Windows Update for Business policies, configuring update rings with deferral periods, deadlines, and active hours. Devices download updates directly from Windows Update or Microsoft Update (or from peers via Delivery Optimization). This approach eliminates the need for WSUS infrastructure.
SCCM manages updates through WSUS integration, providing granular control over which updates are approved, when they deploy, and to which collections. SCCM supports maintenance windows, phased deployments, and detailed compliance reporting. Third-party update catalogs extend patching beyond Microsoft products.
Verdict: Windows Update for Business through Intune is simpler and requires no infrastructure. SCCM provides more granular control and superior third-party patching. Many organizations use co-management to transition update workloads gradually.
OS Deployment
Intune uses Windows Autopilot for device provisioning. Autopilot configures devices during the out-of-box experience (OOBE), joining them to Entra ID, enrolling them in Intune, and applying configurations and applications automatically. Autopilot requires the OEM to register device hardware hashes and does not perform traditional imaging.
SCCM uses Task Sequences for OS deployment, supporting PXE boot, bootable media, and network-based imaging. Task sequences can deploy custom Windows images, install drivers, configure settings, install applications, and execute scripts—all in a defined sequence. This approach is essential for organizations that need custom images or bare-metal deployment.
Verdict: Autopilot is the modern approach for new device provisioning and works well for standard configurations. SCCM Task Sequences remain necessary for bare-metal imaging, custom image deployment, and complex provisioning scenarios in manufacturing or specialized environments.
Compliance and Conditional Access
Intune integrates directly with Microsoft Entra Conditional Access, creating a powerful zero-trust enforcement model. Devices must meet compliance policies (encryption enabled, OS version current, antivirus active) before accessing corporate resources like Microsoft 365, email, or line-of-business applications.
SCCM offers compliance baselines and configuration items that evaluate device state, but it lacks native conditional access integration. Through co-management, SCCM compliance data can feed into Intune for conditional access evaluation.
Verdict: Intune’s conditional access integration is a significant advantage for organizations implementing zero-trust security. This capability alone drives many organizations toward Intune or co-management.
Co-Management: Using Both Together
Co-management allows you to manage devices with both SCCM and Intune simultaneously. The Configuration Manager client and Intune MDM enrollment coexist on the same device, and you control which workloads are managed by which platform.
Co-Management Workloads
You can shift these workloads independently from SCCM to Intune:
- Compliance policies — Device compliance evaluation
- Device configuration — Configuration profiles and policies
- Windows Update policies — Update rings and feature update deployments
- Resource access policies — VPN, Wi-Fi, email, and certificate profiles
- Endpoint Protection — Microsoft Defender settings
- Client apps — Application deployment
- Office Click-to-Run apps — Microsoft 365 Apps management
Why Co-Management Matters
Co-management provides a phased migration path from SCCM to Intune. Rather than an abrupt cutover, you can:
- Enable co-management across your device fleet
- Shift low-risk workloads (compliance, Windows Update) to Intune first
- Validate that Intune management meets your requirements for each workload
- Gradually shift remaining workloads as confidence and capability grow
- Eventually decommission SCCM infrastructure when all workloads are cloud-managed
This approach reduces risk and allows your team to build Intune expertise incrementally.
Licensing
Intune Licensing
Microsoft Intune is included in:
- Microsoft 365 E3 / E5
- Microsoft 365 F1 / F3
- Enterprise Mobility + Security (EMS) E3 / E5
- Microsoft Intune Plan 1 (standalone)
- Microsoft Intune Plan 2 (add-on for advanced features)
- Microsoft Intune Suite (add-on for premium capabilities including Remote Help, Tunnel, and advanced analytics)
Most organizations already have Intune licensing through their Microsoft 365 enterprise agreements.
SCCM Licensing
SCCM requires:
- System Center license (per-core or per-OS environment), OR
- Intune license — any Intune-entitled license also grants rights to use Configuration Manager through co-management
Since Microsoft 365 E3/E5 licenses include Intune, most enterprise customers already have ConfigMgr use rights. However, the infrastructure costs (servers, SQL licensing, networking) are separate.
Migration Path: SCCM to Intune
For organizations planning to move from SCCM to Intune, this migration path minimizes disruption:
Phase 1: Assessment and Planning (4-8 weeks)
- Inventory all SCCM-managed workloads and configurations
- Identify endpoint management requirements that must be met in Intune
- Map SCCM configurations to Intune equivalents
- Identify gaps where Intune does not yet match SCCM capabilities
- Design the target-state Intune configuration
Phase 2: Enable Co-Management (2-4 weeks)
- Configure Entra ID hybrid join or cloud-native join
- Enable co-management in SCCM
- Enroll devices in Intune through co-management
- Verify dual management is functioning correctly
Phase 3: Workload Migration (3-6 months)
- Shift compliance policies to Intune and validate conditional access
- Migrate Windows Update management to Windows Update for Business
- Transition endpoint protection to Intune-managed Microsoft Defender
- Move device configuration profiles to Intune
- Migrate application deployment to Intune
Phase 4: Decommission SCCM (2-4 weeks)
- Verify all workloads are fully managed by Intune
- Remove Configuration Manager client from devices
- Decommission SCCM site servers and infrastructure
- Redirect IT team training and processes to Intune administration
Pros and Cons Summary
Microsoft Intune
Pros:
- No on-premises infrastructure to maintain
- Native cloud management—devices manageable from anywhere
- Strong multi-platform support (Windows, macOS, iOS, Android, Linux)
- Conditional access integration for zero-trust security
- Rapid feature development with monthly service updates
- Simplified operations for IT teams
Cons:
- Less granular control for certain advanced Windows management scenarios
- No bare-metal OS deployment (Autopilot requires functional OS)
- Application deployment less flexible than SCCM task sequences
- Reporting capabilities still maturing compared to SCCM’s SQL-based reporting
- Requires reliable internet connectivity for management operations
SCCM (Configuration Manager)
Pros:
- Deep Windows management capabilities refined over 20+ years
- Comprehensive OS deployment with task sequences
- Advanced application deployment with complex dependency handling
- Detailed reporting and software metering
- Works in air-gapped or limited-connectivity environments
- Granular control over update deployment timing and targeting
Cons:
- Significant on-premises infrastructure requirements
- High operational overhead for server maintenance and updates
- Limited multi-platform support
- No native conditional access integration
- Declining investment from Microsoft relative to Intune
- Requires specialized expertise to manage effectively
FAQ
Is Microsoft deprecating SCCM? Microsoft has not announced an end-of-life date for Configuration Manager. It continues to receive feature updates through the current branch. However, Microsoft’s strategic investment is clearly focused on Intune, and the long-term direction is cloud-native management. Organizations should plan their migration timeline accordingly rather than waiting for a deprecation announcement.
Can Intune replace SCCM completely? For most organizations, yes—Intune can now handle the majority of endpoint management workloads. However, organizations that rely heavily on bare-metal OS deployment, complex task sequences, or advanced software distribution may find gaps. Co-management allows you to identify these gaps before committing to a full migration.
What is the difference between Intune and Microsoft Endpoint Manager? Microsoft Endpoint Manager (MEM) was a branding umbrella that included both Intune and Configuration Manager. Microsoft retired the MEM branding in 2023, and the products are now simply called Microsoft Intune (cloud) and Microsoft Configuration Manager (on-premises). The Intune admin center is the unified console for cloud management.
How long does an Intune migration take? A typical SCCM-to-Intune migration takes 6-12 months for a mid-sized organization. This includes assessment, co-management enablement, workload migration, and SCCM decommissioning. Larger enterprises with complex environments may require 12-18 months. The co-management approach allows you to migrate incrementally without disrupting operations.
Does Intune work without internet connectivity? Intune requires internet connectivity for device management, policy delivery, and application deployment. Devices that go offline temporarily will continue operating with their last-received policies. However, environments with extended periods of no connectivity—such as field operations or classified networks—should retain SCCM or alternative on-premises management.
Can I manage servers with Intune? Intune is designed for endpoint management (desktops, laptops, mobile devices). While Windows Server can technically enroll in Intune, it is not the intended use case and lacks server-specific management capabilities. For server management, use Azure Arc, Configuration Manager, or dedicated server management tools.
What training does my IT team need for Intune? IT professionals transitioning from SCCM to Intune should focus on Microsoft Entra ID fundamentals, Intune device management and app deployment, Windows Autopilot, conditional access policies, and PowerShell for Intune automation (Microsoft Graph API). The Microsoft Certified: Endpoint Administrator Associate (MD-102) certification covers these areas comprehensively.