What Is Microsoft Intune? Features, Limitations, and Alternatives

Microsoft Intune is the cloud-based endpoint management platform at the center of Microsoft's device strategy. It handles mobile device management (MDM), mobile application management (MAM), and policy enforcement across Windows, macOS, iOS, and Android. If you're evaluating endpoint management tools, you need to understand what Intune actually does well and where it leaves gaps that other tools need to fill.

Intune is Microsoft's cloud-native replacement for on-premises device management. It runs in Azure and gives IT administrators a browser-based console for enrolling, configuring, and securing endpoints without requiring on-premises infrastructure or VPN connections.

At its core, Intune handles three categories of work:

• Device management - Enroll corporate and personal devices, push configuration profiles, and enforce compliance policies through integration with Microsoft Entra ID (formerly Azure Active Directory).

• Application management - Deploy apps from public stores (Apple App Store, Google Play, Microsoft Store) and push line-of-business apps to managed devices. Intune also supports app protection policies for BYOD scenarios where the device itself isn't enrolled.

• Compliance and conditional access - Define rules for OS version, encryption status, and other security requirements. Devices that fall out of compliance can be blocked from accessing corporate resources through conditional access policies in Entra ID.

Intune also provisions new Windows devices through Windows Autopilot, allowing IT teams to ship laptops directly to end users without imaging them first.

Intune has evolved significantly. In 2023, Microsoft consolidated its endpoint management products under the Microsoft Intune Suite brand, replacing the older Microsoft Endpoint Manager (MEM) umbrella. The rebrand brought several add-on capabilities under one licensing structure. For background on the MEM-to-Intune transition, see the Microsoft Endpoint Manager explainer.

Key changes since 2022 include:

• Microsoft Intune Suite (March 2024) - A premium add-on bundle that includes remote help, endpoint privilege management, advanced analytics, and cloud PKI.

• Linux enrollment - Intune now supports enrolling Ubuntu and Red Hat Enterprise Linux (RHEL) desktops, though management depth is limited compared to Windows.

• Platform SSO for macOS - Improved macOS onboarding experience that reduces friction for Mac users in Entra ID environments.

• Copilot in Intune - AI-assisted policy recommendations and troubleshooting integrated into the admin console.

• Custom compliance scripts - Support for writing custom compliance detection logic beyond built-in policies.

These updates address some long-standing complaints but don't fundamentally change Intune's approach: it remains a policy-driven MDM, not a patch management platform.

Intune covers a broad set of platforms, but the depth of management varies significantly by OS:

The most significant gaps are Windows Server (not supported at all) and macOS patching. Intune can delay macOS update visibility and nudge users to install updates, but it can't enforce installation or manage reboots the way it does on Windows.

This is one of the most common questions IT teams ask, and the answer hasn't changed much. Intune was designed to manage Microsoft products. Third-party application patching is limited.

You can deploy Win32 apps and update them through Intune, but there's no automated third-party patch detection or deployment workflow built in. If you want to keep Chrome, Zoom, Slack, Adobe Reader, or any other third-party app current across your fleet, you need to either build custom detection scripts, use the Microsoft Store for Business (which Microsoft deprecated in 2024), or purchase a third-party patching add-on.

According to the Ponemon Institute, third-party applications account for up to 76% of vulnerabilities found on the average endpoint. Leaving those unpatched because your management tool doesn't cover them creates real risk.

Intune isn't sold as a standalone product for most organizations. It's bundled into Microsoft enterprise agreements. To get Intune, you need one of the following:

• Microsoft 365 E3 or E5

• Microsoft 365 Business Premium

• Microsoft 365 F1 or F3

• Enterprise Mobility + Security (EMS) E3 or E5

• Microsoft 365 Government G3 or G5

• Microsoft Intune Plan 1 (standalone, $8 per user per month)

• Microsoft Intune Plan 2 (add-on for advanced features)

• Microsoft Intune Suite (premium add-on, $10 per user per month on top of Plan 1)

Licensing gets complicated quickly. The Intune Suite add-on bundles features like remote help, tunnel for MAM, and endpoint privilege management that were previously separate purchases. If you need these capabilities, costs add up. For a 500-user organization on E3 licensing, adding the Intune Suite brings the endpoint management cost alone to roughly $9 per user per month before factoring in the E3 license itself.

You also need Microsoft Entra ID P1 or P2 for conditional access and automatic MDM enrollment, which comes with E3/E5 but not all license tiers.

Intune works well for what it was built to do: managing modern Windows and mobile devices in a Microsoft-first environment. It starts to show gaps when your needs extend beyond that scope.

No Windows Server management. If you run Windows Server, Intune doesn't help. You'll still need SCCM, Azure Arc, or another tool. Many organizations end up running SCCM alongside Intune in co-management mode, which adds operational complexity.

Shallow macOS patching. Intune can't enforce macOS updates or manage reboots. If timely macOS compliance matters to your security program, you need a dedicated solution.

No automated third-party patching. The lack of native third-party patch management means most organizations bolt on additional tools, increasing cost and complexity.

Limited Linux support. While Intune now enrolls Ubuntu and RHEL, the management capabilities are minimal compared to what's available for Windows or even macOS.

Remote management gaps. Intune doesn't offer built-in remote control or terminal access. The Intune Suite's Remote Help feature addresses this partially but requires the premium add-on and only works on Windows and Android.

Intune and Automox serve different functions, and many organizations use both. Intune is an MDM platform focused on device enrollment, policy enforcement, and conditional access. Automox is a cloud-native endpoint management platform focused on patching, configuration, and remediation across all major operating systems.

The practical difference: Intune tells you which devices are enrolled and whether they meet your compliance policies. Automox ensures those devices are actually patched and configured correctly, including the third-party software and non-Windows systems that Intune doesn't cover.

For organizations that run Intune for MDM and conditional access, Automox fills the patching and configuration gaps. You don't have to choose one or the other.

Many organizations run SCCM and Intune together using Microsoft's co-management feature. Co-management lets you gradually migrate workloads from SCCM to Intune while keeping both tools active.

This approach makes sense during a transition period, but it introduces its own complexity. You're maintaining two management planes, two policy sets, and two consoles. Devices can receive conflicting instructions if workload ownership isn't carefully defined.

For a full comparison of SCCM capabilities and limitations, see the SCCM deep dive. And if you're evaluating the total cost of maintaining on-premises infrastructure alongside Intune, the cost analysis of on-prem patch management breaks down the numbers.

• Microsoft, "Microsoft Intune planning guide," Microsoft Learn, 2025. https://learn.microsoft.com/en-us/mem/intune/fundamentals/intune-planning-guide

• Microsoft, "What's new in Microsoft Intune," Microsoft Learn, 2025. https://learn.microsoft.com/en-us/mem/intune/fundamentals/whats-new

• Ponemon Institute, "Costs and Consequences of Gaps in Vulnerability Response," ServiceNow/Ponemon, 2019. https://www.servicenow.com/lpayr/ponemon-vulnerability-survey.html

• Microsoft, "Microsoft Intune Suite," Microsoft Learn, 2024. https://learn.microsoft.com/en-us/mem/intune/fundamentals/intune-add-ons