To update a third-party app with Intune, first identify whether it is a Microsoft Store app, an Enterprise App Catalog app, or a manually packaged Win32 app. The update method depends on that app type and its assignment: Enterprise App Catalog auto-update applies only to catalog apps assigned as Required, while other apps follow Store update behavior or an administrator-managed supersedence workflow.
Identify what “Windows Catalog App” means in your tenant
That phrase can refer to different app-management routes in Intune, and they do not share one update process. Check the app’s type and how it is assigned before changing anything:
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- Microsoft Store app: Store-based deployment, with different update behavior for UWP and Win32 apps.
- Enterprise App Catalog app: A catalog app managed through Enterprise App Management; it may be set to auto-update or updated through a reviewed supersedence workflow.
- Manually packaged Win32 app: An administrator uploads an
.intunewinpackage, configures it, and manages later versions through assignments and, if appropriate, supersedence.
Microsoft’s Enterprise App Management documentation describes catalog-app management as available standalone or in the Intune Suite. The cited documentation does not establish current pricing.
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| Workflow | Which apps | Who controls an update | Assignment and rollout |
|---|---|---|---|
| Store updates | Microsoft Store apps | Store policy affects UWP updates; Intune manages Store Win32 updates. | For Store Win32, Required lets Intune manage the app. With Available, a user must first select Install in Company Portal. |
| Enterprise App Catalog auto-update | Enterprise App Catalog apps only | Intune applies a newer catalog version when auto-update is enabled. | Requires a Required assignment on Windows 10 or Windows 11; no rollout rings or phased deployment. |
| Guided update supersedence | Catalog apps with an available update | An administrator reviews the update and creates a superseding app. | Review and set assignments on the replacement app; some settings are not copied. |
| Manually packaged Win32 supersedence | Win32 apps managed in Intune | An administrator packages and configures the new version. | The superseding app must be explicitly targeted; assignment controls deployment. |
Sources: Microsoft’s Store app guidance, Enterprise App Management documentation, guided update supersedence instructions, Win32 supersedence guidance, and Win32 app deployment instructions.
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Update Microsoft Store apps
UWP apps
Microsoft says Store apps deployed through Intune are automatically kept current. For UWP apps, that automatic behavior depends on not enabling the policy that turns off automatic downloading and installing of updates. Check whether that policy is enabled if a UWP app is not receiving updates. See Add Microsoft Store apps to Microsoft Intune.
Store Win32 apps
Microsoft’s documentation currently marks Microsoft Store Win32 app availability as preview. Not every app is available or searchable, and publishers host installer content on their own infrastructure. A Required assignment lets Intune manage the app. For an Available assignment, the user must first choose Install in Company Portal; Intune then takes over management and automatic updates. Store Win32 updates are handled by Intune and are not affected by Store update policies. Check the current Microsoft Store app documentation for availability and setup details.
Use Enterprise App Catalog auto-update for Required apps
For a catalog app assigned as Required, enabling auto-update lets Intune check for a newer catalog version and apply it to targeted devices. This avoids creating a new app and supersedence relationship for each version. Microsoft documents this feature for Windows 10 and Windows 11 and for Enterprise App Catalog apps only; an Available assignment retains the existing update workflow. Details are in Microsoft’s Enterprise Application Management documentation.
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This is the hands-off option, but it does not offer rollout rings or staged deployment: the new version goes to all targeted devices at once. Auto-update also does not provide rollback or automatic uninstall remediation. Microsoft’s documentation states, “Auto-update doesn’t support rollout rings or deployment plans for staged update deployment.” If a problem requires remediation, an administrator must take a separate action, such as an Uninstall assignment or a script. See Enterprise App Management.
Review a catalog update before deploying it
If you need an approval point before updating, use guided update supersedence instead of automatic application. Microsoft’s documented flow is to view available updates, select Update, then choose Supersede app to create a new app with the latest package and a supersedence relationship.
- Open the catalog app’s available updates in Intune.
- Select Update, then Supersede app.
- Review the new app’s settings. Some settings, including scope tags and assignments, are not copied.
- Set or confirm the replacement app’s assignments before creating it, then manage deployment through that app.
Microsoft’s service-level objectives say most catalog updates are available within 24 hours of vendor release, while updates requiring manual validation are typically available within seven days. These are service objectives, not guarantees for every vendor update. Microsoft documents the workflow and timing in Guided Update Supersedence for Enterprise App Management, updated April 14, 2026.
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Update a manually packaged Win32 app with supersedence
For an app that is not being updated through the Store or Enterprise App Catalog, prepare a new .intunewin package, configure its installer commands and detection rules, and assign it. Intune’s Win32 app deployment guide covers adding and assigning the package.
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When configuring supersedence, decide whether the new installer updates the installed version itself or whether the old app must be removed first. If the newer installer updates the old version, an uninstall command is not necessary; if the new app replaces the old one, uninstalling the previous version may be necessary. Explicitly target the superseding app: Microsoft says the agent ignores a superseding app without targeting. See Add Win32 app supersedence.
Account for catalog update limits
- Version display can lag: Enterprise App Catalog data may be cached for up to one hour.
- Reporting is not a full audit trail: Catalog update reporting reflects the latest state, not a history of earlier versions or actions.
- Some apps update themselves: Self-updating catalog apps follow the vendor’s process and may require tenant network rules that allow vendor access.
- Licensing is the customer’s responsibility: Catalog apps may require a vendor license. Intune does not perform a license check.
These limits and requirements are documented in Microsoft’s Enterprise Application Management guidance.
Learn the catalog workflow
Microsoft Learn’s Manage Enterprise App Catalog Applications training module covers deploying catalog apps, monitoring updates, and using supersedence.
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