^{Originally published on May 14, 2024}

Choosing between Microsoft Intune and System Center Configuration Manager (SCCM) isn’t just about tools—it’s about how your organization manages risk, supports remote workers, and stays compliant.

The twist? You might not have to choose just one.

Intune and SCCM, defined

• Microsoft Intune is a cloud-based Mobile Device Management (MDM) and Mobile Application Management (MAM) platform.
  
• System Center Configuration Manager (SCCM) is a traditional, on-premises endpoint management solution.
  

Both are part of Microsoft’s broader Endpoint Manager family—but they shine in different situations.

What’s trending in 2025 (and why it should shape your decision)

If you’re evaluating Intune vs. SCCM in isolation—without factoring in where the industry’s headed—you might be solving yesterday’s problems. The truth is, endpoint management is changing fast, and what’s trending now should absolutely shape your next move.

Here’s what we’re seeing:

Co-management is the new normal.
Organizations aren’t choosing either Intune or SCCM—they’re blending them. Co-management lets you run both tools side-by-side, gradually shifting workloads to the cloud without ripping out legacy infrastructure. If you’re not ready to go full cloud, this gives you runway—and flexibility.

Cloud PKI is gaining serious traction.
Intune’s new Cloud PKI (Public Key Infrastructure) capabilities make certificate-based authentication more accessible—without the headaches of managing on-prem CAs (Certificate Authorities). If certificate-based Wi-Fi, VPN, or app access is in your future (spoiler: it probably is), Intune has the edge.

Zero Trust and Conditional Access are now table stakes.
Security frameworks like Zero Trust aren’t optional anymore—they’re baseline. Intune is purpose-built for enforcing these policies dynamically across devices and identities. SCCM? Not so much. If you're prioritizing real-time enforcement and adaptive access, Intune’s native integrations win.

Automation is everything.
Manual patching, compliance checks, app assignments—it all scales better with automation. Intune is leaning into that future with more orchestration tools, templated policies, and streamlined onboarding flows. If your IT team is stretched thin, these capabilities can be the difference between “keeping up” and constantly playing catch-up.

Bottom line:
The trends aren't just nice-to-know—they’re flashing neon signs pointing toward a more cloud-centric, policy-driven future. If your long-term strategy includes agility, better security posture, and simplified ops, Intune (or co-management with SCCM) is the direction to lean.

Key comparison: Intune vs SCCM

So... which one is “better”?

Let’s be honest: “better” depends on your reality.
Got legacy servers? Remote workers on every continent? A compliance checklist the size of a novel?

Let’s walk through the tradeoffs like real IT pros.

Intune (Cloud-based MDM/MAM)

Best for: Cloud-first orgs managing laptops, phones, tablets
Works across: Windows, macOS (Apple), iOS, Android, iPadOS, and Linux
Highlights:

• Streamlined deployment, updates, app protection policies
  
• Integrated with Microsoft Defender for Endpoint
  
• Self-service portal for users
  
• Strong automation for policies, compliance, and conditional access
  

Intune limitations:

• No server OS support
  
• Complexity and licensing complaints
  
• Remote provisioning features can be buried or gated
  

Intune is modern, nimble, and built for today’s remote reality—but it still struggles when the workload shifts to legacy systems, back-end infrastructure, or complex app deployments.

What Intune Does Best in a Nutshell

If your team is remote, hybrid, or just allergic to VPNs, Intune is your go-to. It’s built for managing today’s device zoo—Windows laptops, iPhones, Androids, Macs, even the odd Linux machine. Everything’s handled through the cloud, which means no on-prem infrastructure, and you get tight integration with Microsoft Defender and Entra ID (formerly Azure AD) baked right in. IT can push updates, enforce compliance, configure apps, and set conditional access policies without physically touching a device. Plus, users get a self-service portal so they can do basic actions themselves—less ticket churn for the helpdesk.

That said, Intune isn’t perfect. It doesn’t support server OS, which is a deal-breaker for some orgs. And while it’s powerful, parts of the admin experience can feel buried behind menus—or locked behind premium SKUs. Licensing isn’t exactly intuitive either. Still, if your device fleet is modern and your team wants to manage things from anywhere, Intune’s a strong bet.

SCCM (On-prem PC + Server Management)

Best for: Enterprises needing tight control over desktops, servers, and update compliance
Works best with: Microsoft-heavy environments
Highlights:

• Simultaneous large-scale software deployments
  
• Patch and update automation
  
• Remote access and troubleshooting
  
• Built-in OS deployment support
  
• Application support includes Microsoft App-V, Med-V, Citrix XenApp, Forefront
  

SCCM limitations:

• Limited non-Windows device support
  
• Licensing is complex and costly
  
• Requires more on-prem infrastructure and maintenance
  

SCCM still thrives in high-control, compliance-heavy environments, especially those that can’t go all-in on cloud. But it comes with heavier operational baggage and licensing gotchas.

What SCCM Does Best in a Nutshell

Now, if your environment leans more traditional; with data center roots, on-prem servers, and a need for complete control, SCCM is still very much in the game. It excels at managing desktops and servers at scale, with mature workflows for pushing patches, deploying operating systems, and handling complex applications like Microsoft App-V, Citrix XenApp, and Forefront. SCCM also lets you reach into a device remotely for diagnostics and remediation, which comes in handy when something goes sideways.

But SCCM isn’t without its drawbacks. It doesn’t play as nicely with non-Windows devices, it needs a fair bit of care and feeding (infrastructure-wise), and licensing can be, frankly, painful. Still, if you need that deep level of control over your Windows estate and you have the resources to support it—SCCM delivers.

BYOD and hybrid work? You’ll probably need both

Bring-Your-Own-Device (BYOD) policies and hybrid work models are here to stay. That means managing a mix of corporate laptops, personal phones, random tablets, and maybe even a stray Linux box.

Here’s the kicker:

• MDM helps protect the device
  
• MAM helps protect the apps and data
  

Intune handles both well. But SCCM handles deep patching and legacy Windows infrastructure better. That’s why many enterprises go co-managed and use both tools side by side.

Still wondering which one to pick?

• Go with Intune if you're modern, mobile, and cloud-ready
  
• Stick with SCCM if you’re managing servers, need tight control, or run older systems
  
• Use both if you're somewhere in between (which, let’s face it, is most of us)
  

Let’s figure it out together

Hypershift has helped hundreds of IT teams make the leap, whether that’s cloud-first with Intune, grounded with SCCM, or a strategic blend of both.

Check out our Managed Services to see more of what we can offer.

Book a call with our Microsoft experts and we’ll help you build the right roadmap.