Understanding the Landscape: Intune and SCCM in 2026
Microsoft's device management strategy has undergone a fundamental shift. SCCM (System Center Configuration Manager), now officially called Microsoft Configuration Manager, has been the enterprise device management standard for over two decades. It provides deep, granular control over Windows devices through an on-premises infrastructure of site servers, management points, distribution points, and SQL databases.
Microsoft Intune, by contrast, is a cloud-native endpoint management service that requires zero on-premises infrastructure. It manages devices through MDM (Mobile Device Management) and MAM (Mobile Application Management) protocols, supporting Windows, macOS, iOS, Android, and Linux from a single cloud console.
The question most enterprise IT leaders face is not "which is better" — it is "when do we move, how fast, and what do we keep?" This guide provides the data-driven framework for making that decision. For organizations evaluating their broader Microsoft 365 strategy, device management is a critical component that affects security posture, user experience, and operational costs.
Feature Comparison: Intune vs SCCM
| Capability | Microsoft Intune | SCCM (ConfigMgr) |
|---|---|---|
| Infrastructure | Cloud-only, no on-prem servers | On-premises site servers, SQL, DPs |
| OS Platforms | Windows, macOS, iOS, Android, Linux | Windows (primary), limited macOS/Linux |
| Device Provisioning | Windows Autopilot, Apple DEP, Android Zero-Touch | Task sequences (OSD), PXE boot, media |
| Application Deployment | Win32 apps, LOB, MSIX, Store, web apps | Full application model with dependencies, sequencing, supersedence |
| Software Updates | Windows Update for Business, expedited updates | WSUS integration, detailed update groups, maintenance windows |
| Compliance Policies | Native, integrates with Conditional Access | Configuration baselines, limited CA integration |
| Endpoint Security | Built-in: antivirus, firewall, encryption, ASR | Endpoint Protection role, Windows Defender integration |
| Conditional Access | Full native integration with Entra ID | Requires co-management or hybrid setup |
| Reporting | Cloud-based, improving but less granular | Extensive SQL-based, custom SSRS reports |
| Server Management | Not supported | Full server management capabilities |
| Remote Control | Remote Help (add-on), third-party integration | Built-in remote control |
| Licensing | Per user, included in M365 E3/E5 | Per core + infrastructure costs |
Cloud-Only vs Hybrid: Choosing Your Management Model
Cloud-Only with Intune
A cloud-only model with Intune is the right choice when your organization meets these criteria:
- Primarily remote or hybrid workforce with devices that connect over the internet
- No requirement for complex OS deployment task sequences (Autopilot covers your provisioning needs)
- Application portfolio that can be packaged as Win32 apps, MSIX, or delivered via Microsoft Store
- No on-premises server management requirements (or servers managed by separate tools)
- macOS, iOS, and Android devices alongside Windows that need unified management
- Strong desire to eliminate on-premises infrastructure costs and complexity
The cloud-only model eliminates the need for site servers, distribution points, SQL Server instances, and the IT staff time required to maintain SCCM infrastructure. For a 5,000-device environment, this typically saves $150,000-$300,000 annually in infrastructure and personnel costs.
Hybrid with Co-Management
Co-management is the bridge between SCCM and Intune. It allows both solutions to manage the same device simultaneously, with individual workloads assigned to either SCCM or Intune. This provides a gradual migration path without the risk of a big-bang cutover.
Co-management workloads that can be shifted to Intune independently:
- Compliance policies — Move first; enables Conditional Access integration immediately
- Device configuration — Configuration profiles in Intune replace many SCCM configuration baselines
- Windows Update policies — Windows Update for Business through Intune replaces SCCM/WSUS-based patching
- Endpoint Protection — Intune's endpoint security profiles provide comprehensive Defender management
- Resource access — Wi-Fi, VPN, email, and certificate profiles managed through Intune
- Office Click-to-Run apps — Microsoft 365 Apps deployment and updates through Intune
- Client apps — Move last; this is typically the most complex workload to migrate
The Co-Management Migration Path
Phase 1: Enable Co-Management (Weeks 1-4)
Prerequisites: Azure AD Hybrid Join configured, Intune licenses assigned, SCCM updated to current branch. Enable co-management in the SCCM console under Cloud Services > Co-management. Start with a pilot collection of 50-100 devices.
Initial workload assignment: keep all workloads on SCCM except compliance policies, which should be the first workload moved to Intune. This immediately enables Conditional Access based on Intune compliance state, providing tangible security value from day one.
Phase 2: Shift Quick-Win Workloads (Weeks 4-12)
Move device configuration, Windows Update policies, and Endpoint Protection workloads to Intune. These are relatively low-risk transitions because Intune's capabilities in these areas are mature and well-documented. Monitor the pilot group for 2-4 weeks per workload before expanding to the full environment.
Phase 3: Application Migration (Weeks 12-24)
This is the most complex phase. Inventory all SCCM applications and categorize them by deployment complexity:
- Simple — Single MSI or EXE with straightforward install/uninstall commands. These migrate directly to Intune Win32 app management
- Moderate — Applications with dependencies or specific installation order requirements. Package with detection rules and dependency chains in Intune
- Complex — Applications requiring task sequence-level orchestration, custom scripts, or multiple interdependent installations. These may need to remain on SCCM or be repackaged for Intune compatibility
Phase 4: Autopilot Deployment (Weeks 16-28)
Replace SCCM OS deployment with Windows Autopilot for new device provisioning. Register device hardware hashes with the Autopilot service, create deployment profiles (user-driven for standard deployments, self-deploying for kiosks), and configure Enrollment Status Page settings that ensure critical applications and policies are applied before the user reaches the desktop.
Autopilot pre-provisioning (formerly white glove) allows IT to prepare devices in advance — the device downloads policies and applications in a staging environment so the end user experiences a faster first-boot experience.
Phase 5: SCCM Decommission (Weeks 24-48)
Once all workloads have been migrated and validated on Intune, plan the SCCM decommission. This involves removing the SCCM client from all devices (the co-management agent makes this seamless), decommissioning distribution points, site servers, and the site database, reclaiming server infrastructure (or terminating cloud-hosted VMs), and updating documentation and operational procedures.
Licensing: Understanding the Cost Model
The licensing model is fundamentally different between Intune and SCCM, and understanding this difference is critical for budget planning:
| License | Intune Included? | Approximate Cost/User/Month |
|---|---|---|
| Microsoft 365 E3 | Yes (Intune Plan 1) | $36 |
| Microsoft 365 E5 | Yes (Intune Plan 1) | $57 |
| EMS E3 | Yes (Intune Plan 1) | $10.60 |
| EMS E5 | Yes (Intune Plan 1) | $16.40 |
| Intune Plan 1 (standalone) | Yes | $8 |
| Intune Plan 2 (add-on) | Advanced features | $4 add-on |
| Intune Suite (add-on) | Full suite with Remote Help, Tunnel, etc. | $10 add-on |
Intune Plan 2 and the Intune Suite add-on provide advanced capabilities including Microsoft Tunnel for mobile VPN, Remote Help for remote assistance, endpoint privilege management, advanced endpoint analytics, and firmware-over-the-air updates for specialized devices.
SCCM licensing requires System Center licenses (per-core model) plus the hidden costs of on-premises infrastructure: Windows Server licenses for site servers and distribution points, SQL Server licenses for the site database, storage and networking infrastructure, and IT personnel time for maintenance, patching, and troubleshooting. These costs frequently exceed the visible license costs by 2-3x.
Conditional Access: The Security Game-Changer
Conditional Access is arguably the most compelling reason to move to Intune, and it is an area where SCCM simply cannot compete without co-management. Conditional Access policies in Microsoft Entra ID can require that devices be Intune-enrolled and compliant before accessing corporate resources (email, SharePoint, Teams, custom applications).
This creates a zero-trust security model where every access request is evaluated against device health, user identity, location, and risk level. A device that is not compliant with security policies — missing patches, no disk encryption, outdated antivirus — is blocked from accessing corporate data until remediated. This is transformative for security in remote and hybrid work environments where traditional network perimeter controls are ineffective.
Conditional access policies can be granular: require MFA for risky sign-ins, block access from non-compliant devices, restrict downloads on unmanaged devices to browser-only (no sync or download), and enforce app protection policies on personal devices. This level of policy enforcement is native to Intune and cannot be replicated with SCCM alone.
Endpoint Analytics: Data-Driven Device Management
Endpoint analytics in Intune provides visibility into device performance, application reliability, and user experience metrics that SCCM's reporting cannot match without significant customization. Key metrics include startup performance scores (boot time, sign-in time, desktop ready time), application reliability (crash rates, hang rates, per-application health), and proactive remediations that automatically detect and fix common issues before users report them.
These insights enable IT teams to make data-driven decisions about hardware refresh cycles, application modernization priorities, and policy changes that affect user productivity. Proactive remediations run PowerShell scripts on a schedule to detect and fix issues — stale certificates, registry misconfigurations, storage cleanup — without requiring a helpdesk ticket or user intervention.
Decision Framework: When to Choose What
| Scenario | Recommendation |
|---|---|
| Under 5K devices, cloud-first, remote workforce | Intune only |
| 5K-20K devices, hybrid workforce, some complex apps | Co-management transitioning to Intune |
| 20K+ devices, complex OSD, on-prem servers | Co-management with SCCM for complex workloads |
| Multi-OS (Windows + Mac + mobile) | Intune (only solution managing all platforms) |
| Greenfield / new organization | Intune only (no reason to deploy SCCM) |
| Heavily regulated with complex compliance | Co-management (Intune for CA, SCCM for detailed reporting) |
How EPC Group Approaches Intune Migration
With 29 years of Microsoft consulting experience, EPC Group has guided hundreds of organizations through the SCCM-to-Intune migration journey:
- Environment assessment — Comprehensive inventory of your SCCM environment including applications, task sequences, configuration baselines, compliance settings, and infrastructure topology
- Migration roadmap — Phased migration plan with workload prioritization, risk assessment, and timeline aligned to your organization's capacity for change
- Co-management implementation — Enable co-management with workload-by-workload migration, including pilot testing and validation gates before production rollout
- Autopilot configuration — Design and deploy Windows Autopilot profiles for new device provisioning, including pre-provisioning for IT-prepared deployments
- Conditional Access design — Implement compliance-based Conditional Access policies that enforce zero-trust security across all managed devices
- Application packaging — Repackage SCCM applications for Intune Win32 app management, including detection rules, dependencies, and supersedence relationships
Frequently Asked Questions
Should I migrate from SCCM to Intune or use co-management?
The answer depends on your environment complexity. If you have fewer than 5,000 devices, no legacy Win32 applications requiring complex deployment sequencing, and your workforce is primarily remote or hybrid, a full migration to Intune is the recommended path. For organizations with 10,000+ devices, complex application deployment requirements, operating system deployment (OSD) needs, or on-premises server management, co-management is the pragmatic approach — it lets you shift workloads to Intune incrementally while keeping SCCM for capabilities that Intune does not yet fully match, particularly OS deployment and complex application sequencing.
What is the cost difference between Intune and SCCM?
Intune is licensed per user (not per device) and is included in Microsoft 365 E3, E5, and EMS E3/E5 licenses, typically $8-$12 per user per month as part of these bundles. SCCM requires a System Center license (approximately $1,323 per two-processor core pack for the Datacenter edition) plus the infrastructure costs of on-premises servers, SQL Server licensing, distribution points, and IT staff to maintain the infrastructure. For a 5,000-user organization, the total cost of ownership for Intune-only management is typically 30-40% lower than SCCM when factoring in infrastructure, licensing, and personnel costs over a 3-year period.
Can Intune fully replace SCCM for enterprise environments?
As of 2026, Intune can replace SCCM for approximately 80-85% of enterprise device management scenarios. Intune handles application deployment (Win32, LOB, Microsoft Store, web apps), compliance policies, configuration profiles, Windows Autopilot provisioning, endpoint security (antivirus, firewall, disk encryption, attack surface reduction), and conditional access integration. The remaining gaps where SCCM still has advantages are: complex task sequence-based OS deployment (Intune Autopilot covers most but not all scenarios), complex application deployment with dependencies and sequencing, on-premises server management, and granular software metering and usage reporting.
How long does an SCCM to Intune migration take?
A typical SCCM to Intune migration for a mid-size enterprise (2,000-10,000 devices) takes 6-12 months. Phase 1 (months 1-2) covers assessment, application inventory, and policy mapping. Phase 2 (months 2-4) implements co-management as a bridge, shifting compliance and conditional access workloads to Intune first. Phase 3 (months 4-8) migrates application deployment, device configuration, and endpoint security workloads. Phase 4 (months 8-12) handles OS deployment migration to Autopilot and decommissions SCCM infrastructure. Organizations with complex environments (50,000+ devices, custom task sequences, or multiple SCCM hierarchies) should plan for 12-18 months.
What is Windows Autopilot and how does it replace SCCM OSD?
Windows Autopilot is a cloud-based device provisioning service that replaces traditional OS deployment (OSD) task sequences in SCCM. Instead of imaging devices with a custom OS image, Autopilot configures the factory-installed Windows OS during the out-of-box experience (OOBE). The device connects to the internet, authenticates the user, downloads Intune policies and applications, and is ready for use — typically in 30-60 minutes compared to 2-4 hours for traditional SCCM OSD. Autopilot supports self-deploying mode (for kiosks and shared devices), user-driven mode (for standard deployments), and pre-provisioning (white glove) for scenarios requiring IT preparation before handoff to the user.
Planning an Intune Migration?
EPC Group has guided hundreds of enterprises through SCCM-to-Intune migrations across healthcare, finance, and government. Start with an environment assessment to build your migration roadmap.
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CEO & Chief AI Architect at EPC Group | 29 years Microsoft consulting | Microsoft Press author