Microsoft Intune vs SCCM: Complete Comparison Guide 2026

Microsoft Intune vs SCCM: What's the Difference?

Choosing between Microsoft Intune and SCCM (System Center Configuration Manager, now called Microsoft Endpoint Configuration Manager or MECM) is one of the most critical decisions for enterprise IT teams managing endpoints. Both solutions are now part of Microsoft Endpoint Manager, but they serve different deployment models and use cases.

Microsoft Intune is a cloud-native mobile device management (MDM) and mobile application management (MAM) solution designed for modern, remote-first organizations. It manages devices through cloud policies without requiring on-premises infrastructure.

SCCM/ConfigMgr is a powerful on-premises endpoint management solution with deep Windows management capabilities, complex deployment options, and the ability to manage devices without internet connectivity. It has been the enterprise standard for Windows management for over 20 years.

Key Terminology

SCCM = System Center Configuration Manager (legacy name)
ConfigMgr = Configuration Manager (current shorthand)
MECM = Microsoft Endpoint Configuration Manager (official current name)
MEM = Microsoft Endpoint Manager (unified console for Intune + ConfigMgr)

Deployment Model: Cloud vs On-Premises

The fundamental difference between Intune and SCCM is the deployment architecture. This decision impacts infrastructure costs, management overhead, and which devices you can effectively manage.

Intune: Cloud-Based

No on-premises infrastructure required
Microsoft manages all backend servers
Automatic updates and new features
Global availability through Azure CDN
Scales automatically with device count
Requires internet connectivity for devices

SCCM: On-Premises

Requires servers, SQL database, distribution points
Full control over data location
Manual updates and patching required
Works in air-gapped/isolated networks
Infrastructure scales with complexity
Can manage devices without internet

Infrastructure Requirements Comparison

Component	Intune	SCCM
Primary Server	Microsoft-hosted (Azure)	On-premises site server(s)
Database	Azure SQL (managed)	SQL Server (self-managed)
Content Distribution	Azure CDN / Microsoft Graph	Distribution Points (DPs)
Network Requirements	Internet access required	LAN/WAN, can be isolated
Administration	Intune admin center (web)	ConfigMgr console (Windows app)

Device Management Capabilities

Both Intune and SCCM provide comprehensive device management, but with different strengths and approaches.

Intune Device Management

Enrollment Methods: Windows Autopilot, Apple DEP, Android Enterprise, manual enrollment, bulk enrollment
Configuration Profiles: Device restrictions, Wi-Fi, VPN, email, certificates, custom OMA-URI
Compliance Policies: Define device health requirements, integrate with Conditional Access
Remote Actions: Wipe, retire, restart, sync, remote lock, locate device
BYOD Support: App-level management without full device enrollment (MAM-WE)

SCCM Device Management

Client Deployment: Push installation, manual, GPO, logon scripts, software update point
Configuration Baselines: Compliance settings, remediation scripts, DCM
Hardware/Software Inventory: Detailed asset inventory, custom inventory classes
Remote Control: Full remote desktop control for troubleshooting
Power Management: Wake-on-LAN, power plans, scheduled wake
Endpoint Protection: Integrated antimalware management (Defender)

Operating System Support

A critical difference between Intune and SCCM is the breadth of operating system support. Intune excels at cross-platform management, while SCCM focuses primarily on Windows.

Operating System	Intune	SCCM	Notes
Windows 11/10			Full support on both
Windows Server			SCCM for server management
macOS			Intune has better macOS support
iOS/iPadOS			Intune only for iOS
Android			Intune only for Android
Linux			Intune adds native Linux enrollment
Chrome OS			Limited Intune support

Mobile Device Management

If you need to manage iOS and Android devices, Intune is required. SCCM does not provide native mobile device management. For organizations with mixed Windows/mobile environments, Intune or co-management is essential.

Update Management

Keeping devices updated is critical for security and functionality. Intune and SCCM take different approaches to Windows Update management.

Intune Update Management

Windows Update for Business: Cloud-based update management with deferral policies
Update Rings: Define groups with different update schedules (pilot, broad, critical)
Feature Updates: Control Windows 11/10 feature update rollouts
Quality Updates: Manage monthly security and cumulative updates
Driver Updates: Automatic driver updates via Windows Update
Expedited Updates: Fast-track critical security updates

SCCM Update Management

Software Update Point (SUP): On-premises WSUS integration for update management
Update Groups: Granular control over update deployment timing
Maintenance Windows: Precise scheduling for update installations
Third-Party Updates: Manage non-Microsoft updates (Adobe, Java, etc.)
OS Upgrade Task Sequences: Complex Windows upgrade scenarios
Bandwidth Control: BITS throttling, BranchCache, peer caching

Update Management Recommendation

Intune is ideal for standard Windows Update management with minimal infrastructure. SCCM is better for organizations needing precise control, third-party update management, or complex deployment scenarios with strict maintenance windows.

Application Deployment

Application deployment is a core function of endpoint management. Here is how Intune and SCCM compare for app distribution.

Intune Application Deployment

Microsoft Store Apps: Direct deployment from Microsoft Store for Business
Win32 Apps: Deploy MSI, EXE, MSIX packages with dependency handling
LOB Apps: Custom line-of-business application deployment
iOS/Android Apps: App Store, managed Google Play, enterprise apps
Web Apps: Web clips and PWA deployment
App Protection Policies: MAM policies for app-level data protection
Maximum Package Size: 8 GB for Win32 apps

SCCM Application Deployment

Application Model: Complex apps with multiple deployment types per OS
Packages/Programs: Legacy deployment method for scripts and complex installs
Task Sequences: Complex multi-step installations with dependencies
App-V: Application virtualization support
Software Metering: Track application usage across the organization
User Device Affinity: Install apps based on primary user relationships
Maximum Package Size: Limited only by disk space and network

Security Features

Both platforms integrate with Microsoft's security stack but offer different security management capabilities.

Intune Security Features

Conditional Access: Require device compliance for M365 access
Compliance Policies: Define security baselines
Security Baselines: Pre-configured security settings
Endpoint Security: Antivirus, firewall, disk encryption
Defender for Endpoint: Native integration for EDR
App Protection: Container-based data protection

SCCM Security Features

Endpoint Protection: Defender management and policies
BitLocker Management: Full disk encryption control
Compliance Settings: Configuration baselines
Windows Firewall: Granular firewall policy control
Certificate Deployment: PKI certificate distribution
Script Deployment: Custom remediation scripts

Reporting & Analytics

Visibility into device health, compliance, and deployment status is essential for effective endpoint management.

Intune Reporting

Intune Reports: Built-in reports for devices, apps, compliance
Log Analytics: Azure Monitor integration for advanced analytics
Endpoint Analytics: Device health, startup performance, app reliability
Export to Excel/CSV: Data export for custom reporting
Power BI Integration: Connect Intune data to Power BI dashboards
Microsoft Graph API: Programmatic access to all Intune data

SCCM Reporting

SQL Reporting Services (SSRS): Hundreds of built-in reports
Custom Reports: Build custom SQL-based reports
CMPivot: Real-time query across all managed devices
Status Messages: Detailed deployment and inventory tracking
Power BI Templates: Pre-built dashboards for SCCM data
Asset Intelligence: Software catalog and license management

Licensing & Costs

Understanding the total cost of ownership is critical when comparing Intune and SCCM.

Cost Category	Intune	SCCM
Licensing	Included in M365 E3/E5 EMS E3/E5 Standalone: ~$8/user/month	Windows Server CALs System Center licenses SQL Server licenses
Infrastructure	None (cloud-hosted)	Servers, SQL, storage, network
IT Staff	Lower overhead (no server management)	Higher (infrastructure management)
Training	Moderate (web-based console)	Significant (complex tooling)

Cost Comparison Insight

For organizations already on Microsoft 365 E3 or E5, Intune is included at no additional per-user cost. This makes Intune significantly more cost-effective than maintaining SCCM infrastructure for cloud-ready environments. However, organizations with existing SCCM investments may prefer co-management to protect that investment.

Migration Path: SCCM to Intune

Microsoft provides a clear path for migrating from SCCM to Intune through co-management. This approach allows you to gradually shift workloads while maintaining the capabilities you need.

Co-Management Workloads

With co-management, you can move individual workloads from SCCM to Intune independently:

Compliance Policies: Device compliance and conditional access
Device Configuration: Configuration profiles and settings
Windows Update Policies: Update rings and feature updates
Resource Access Policies: VPN, Wi-Fi, email, certificates
Endpoint Protection: Antimalware and security policies
Client Apps: Application deployment (recommended last)

Recommended Migration Phases

Phase 1: Enable Co-Management (1-2 weeks)

Configure Azure AD Connect, enable hybrid Azure AD join, install Intune connector, enable co-management in SCCM.

Phase 2: Pilot Workloads (2-4 weeks)

Move compliance policies and device configuration to Intune for a pilot group. Validate functionality.

Phase 3: Expand Workloads (4-8 weeks)

Move Windows Updates and Endpoint Protection to Intune. Expand to broader user groups.

Phase 4: Application Migration (8-16 weeks)

Migrate application deployments to Intune. This is typically the most complex phase.

Phase 5: Full Cloud Management (Ongoing)

New devices enrolled directly in Intune via Autopilot. Decommission SCCM infrastructure as legacy devices are retired.

Full Feature Comparison Table

Feature	Intune	SCCM
Deployment & Architecture
Cloud-based management
On-premises management
Air-gapped environment support
Zero infrastructure required
Device Support
Windows 10/11
Windows Server
macOS
iOS/iPadOS
Android
Linux
Deployment Features
Windows Autopilot
OS Deployment (Task Sequences)
Zero-touch provisioning
Bare metal deployment
Application Management
Win32 app deployment
Mobile app deployment
App-V support
App protection policies (MAM)
Software metering
Security & Compliance
Conditional Access integration
Security baselines
Defender for Endpoint integration
BitLocker management

When to Choose: Intune, SCCM, or Both

Choose Microsoft Intune If:

You have a cloud-first or remote-first organization
You need to manage iOS, Android, and macOS devices
You want zero infrastructure to manage
You already have Microsoft 365 E3/E5 licenses
You need Conditional Access for Zero Trust security
You want Windows Autopilot for zero-touch deployment
Your devices always have internet connectivity

Choose SCCM (Configuration Manager) If:

You have complex on-premises infrastructure
You need to manage Windows Server environments
You require air-gapped or isolated network support
You need complex OS deployment with task sequences
You have extensive third-party update requirements
You need software metering and license management
You have existing SCCM expertise and infrastructure

Choose Co-Management (Both) If:

You are transitioning from SCCM to cloud management
You need both cloud and on-premises capabilities
You want Conditional Access while keeping SCCM for complex deployments
You have a hybrid workforce with varying connectivity
You want to protect existing SCCM investments while modernizing

EPC Group Recommendation

For most organizations, we recommend starting with co-management to get the best of both worlds. This allows you to leverage Intune's cloud capabilities (Conditional Access, Autopilot, mobile device management) while maintaining SCCM for complex scenarios. Over time, you can shift more workloads to Intune as your cloud maturity increases.

Frequently Asked Questions

What is the difference between Intune and SCCM?

Microsoft Intune is a cloud-based mobile device management (MDM) and mobile application management (MAM) solution, while SCCM (System Center Configuration Manager, now Microsoft Endpoint Configuration Manager) is an on-premises solution for managing Windows devices. Intune excels at managing mobile devices and remote workforces, while SCCM provides deeper control over on-premises Windows environments with features like OS deployment and complex software distribution.

Can I use Intune and SCCM together?

Yes, Microsoft offers co-management which allows you to use both Intune and SCCM simultaneously. With co-management, devices are managed by both solutions, and you can gradually shift workloads from SCCM to Intune. This is the recommended migration path for organizations transitioning from SCCM to cloud-based management.

Is SCCM being replaced by Intune?

Microsoft is not discontinuing SCCM (Configuration Manager), but the strategic direction is clearly toward cloud-based management with Intune. Microsoft continues to release updates for Configuration Manager and supports co-management scenarios. However, new features and innovation are primarily focused on Intune and the cloud-native approach.

Which is better for Windows 11 management: Intune or SCCM?

Both Intune and SCCM fully support Windows 11 management. Intune offers cloud-native Windows 11 deployment with Windows Autopilot and is ideal for remote/hybrid workforces. SCCM provides more granular control for complex enterprise environments with extensive on-premises infrastructure. Many organizations use co-management to leverage both.

How much does Intune cost compared to SCCM?

Intune is included in Microsoft 365 E3/E5, Enterprise Mobility + Security (EMS), and available standalone at approximately $8/user/month. SCCM licensing is based on Windows Server and System Center licensing, plus infrastructure costs for servers, SQL databases, and distribution points. For organizations already on Microsoft 365 E3/E5, Intune is effectively included at no additional cost.

Can Intune manage on-premises devices?

Yes, Intune can manage on-premises devices that have internet connectivity. Devices do not need to be Azure AD joined; they can be hybrid Azure AD joined (domain-joined with Azure AD registration). However, Intune requires devices to connect to the cloud for policy updates, unlike SCCM which can manage completely air-gapped environments.

What is Microsoft Endpoint Manager?

Microsoft Endpoint Manager is the unified management platform that combines Microsoft Intune and Configuration Manager (SCCM) into a single console. It provides a unified experience for managing all endpoints, whether cloud-managed via Intune or on-premises via Configuration Manager, with seamless co-management capabilities.

How long does SCCM to Intune migration take?

Migration timelines vary significantly based on organization size and complexity. Small organizations (under 500 devices) can complete migration in 2-3 months. Enterprise organizations (5,000+ devices) typically require 6-12 months for a phased co-management approach. EPC Group recommends a workload-by-workload migration strategy rather than a big-bang approach.