Intune patch management is one of the biggest gaps in most Microsoft-only environments. While Intune handles Windows updates and some Microsoft apps well, third-party applications (Chrome, Adobe, 7-Zip, Zoom, etc.) still require separate processes. This guide explains the real options available in 2026, when WinGet is enough, and when you need a proper third-party patching solution.
What Is Intune Patch Management?
Intune patch management refers to keeping all software on managed devices up to date — not just Windows and Microsoft 365 apps. Microsoft Intune natively handles operating system updates and some first-party applications, but it has no built-in catalog or automation for the hundreds of third-party applications that most organizations deploy. This gap in intune patch management is one of the top challenges reported in recent surveys of IT teams.
- Native Intune capabilities cover Windows quality updates, feature updates, and Microsoft 365 apps.
- Third-party apps require either manual Win32 packaging, WinGet, Microsoft’s Enterprise App Catalog (E5), or a dedicated third-party patching solution.
- Without a dedicated process, most MSPs and IT teams end up with a mix of manual scripts, outdated apps, and high support ticket volume for vulnerabilities.
Intune Patch Management Options in 2026
You essentially have four realistic paths for third-party patching with Intune (most of these options are configured and monitored directly in the Intune admin portal):
1. WinGet (Community Repository)
WinGet pulls packages from the public microsoft/winget-pkgs repository. It is free and can work for simple scenarios, but it comes with significant limitations for enterprise use.
- Only clean installs are validated in the pipeline — upgrades are never tested. This is a major weakness for real-world intune patch management.
- No support for transforms, custom switches, or suppressing self-updaters.
- Package maintenance relies on volunteers and bots with no SLA.
- Many packages (especially less popular ones) go stale with no notification.
WinGet is best for developer tooling and long-tail open-source apps on small estates where you can tolerate occasional breakage. For more context on how teams are handling intune patch management challenges in 2026, see the State of Intune 2026 survey results.
2. Microsoft Enterprise App Catalog for Intune Patch Management (E5)
Included with Microsoft 365 E5 (rolled out mid-2026), this is Microsoft’s own curated catalog of third-party apps. For more details on the official offering, see Microsoft’s Enterprise App Catalog documentation.
- Native Intune Win32 apps with proper detection and supersedence.
- Reasonable coverage of common enterprise titles.
- Limited to E5 tenants and a curated list that may not include your specific apps.
3. Manual Win32 Packaging for Intune Patch Management
You (or your team) package every third-party app as .intunewin files with custom detection rules.
- Full control over every setting.
- Extremely high ongoing maintenance cost as versions change.
- Common in small teams but scales poorly for MSPs with multiple clients.
4. Third-Party Patching Solutions (Curated Catalogs)
Commercial solutions (Patch My PC, Automox, etc.) or managed services like Always Up To Date provide pre-packaged, tested updates with ongoing maintenance.
- Upgrade paths are actually tested (not just clean installs).
- Customizations (MSTs, switches, self-updater suppression) persist across versions.
- Dedicated team monitors releases with a published cadence.
- Native Intune Win32 apps with proper reporting.
When to Use WinGet vs Curated Intune Patch Management Solutions
Use this decision framework:
- Use WinGet when: You have a small number of devices, mostly open-source tools, and you have the internal capacity to monitor and fix packages yourself.
- Use Microsoft E5 catalog when: You are already E5 and the apps you need are in their supported list.
- Use a dedicated patching solution when: You manage more than ~50-100 devices, deploy common business apps (Chrome, Acrobat, Zoom, etc.), or need reliable upgrades without constant manual work. Related: How to set up remote support in Intune environments.
The cost of a good patching solution is often lower than the labor cost of maintaining packages manually at scale.
How MSPs Handle Intune Patch Management at Scale
For MSPs, the real problem is not deploying one app once — it is keeping hundreds of third-party applications current across many clients without exploding headcount.
Key requirements for an MSP-grade solution:
- Automatic detection of new versions across a broad catalog.
- Proper supersedence so old versions are retired automatically in Intune.
- Support for ringed deployments and testing groups.
- Clear reporting on patch status per client.
- Ability to apply organization-specific customizations that survive updates.
This is exactly where managed third-party patching services like Always Up To Date deliver value — they handle the packaging, testing, and maintenance so your team can focus on client strategy instead of chasing app updates. See our analysis of the State of Intune 2026 survey for more context on why intune patch management remains such a big challenge for teams.
Frequently Asked Questions
Does Intune support third-party patching natively?
No. Intune has excellent native support for Windows updates and Microsoft 365 apps, but third-party applications require additional tooling (WinGet, manual Win32, Enterprise App Catalog, or a third-party solution).
Is WinGet Enterprise Ready for Intune Patch Management?
WinGet is a distribution mechanism, not an application lifecycle service. It performs basic validation on clean installs but does not test upgrades, uninstalls, or enterprise customizations. Many organizations use it successfully for limited use cases, but it is rarely sufficient as the only patching method for production fleets.
What is the difference between WinGet and Patch My PC for Intune Patch Management?
WinGet uses community-maintained manifests with no SLA or upgrade testing. Curated solutions like Patch My PC maintain their own tested packages, provide proper Intune Win32 apps, and take responsibility for keeping them current and working after deployment.
Should I use Microsoft’s Enterprise App Catalog if I have E5?
It is a good starting point and is already included. However, coverage and testing depth vary. Many MSPs still supplement it with additional solutions for broader app support and more reliable ongoing maintenance.