3rd party developed Custom app suddenly disappears in the Teams client for all users

[benjaminyasoon]

Hi there,
we develop a Custom app integration that is uploaded as a manifest file in the Teams admin center and then deployed via the admin center (https://support.yasoon.com/M365FJ/customer-portal-app#Set-up-guide).

This app will be visible normally here within Teams:

However, for one of our customers this app just vanished from one day to the other since Monday. They used the setup policy to pin the app and they made the app available for everyone.

They also had adjusted there Agents settings because for some reason since a couple of weeks our app is also treated as an "agent" which sometimes causes permission issues. But this is part of another tale....

Can someone help us identify why the app has been disappearing: Is there any setting/option missing? Has Microsoft rolled out any further default behavior lately for custom apps? Is there a Powershell command or anything like that to check on visibility for the app?

Happy to hear back from you!

Best regards,
Benjamin from yasoon (https://yasoon.com/)

[Prasad-MSFT]

Hi @benjaminyasoon, thanks for raising your issue. Could you please check below stepa?

App Permission Policies Changed:
Microsoft has been rolling out changes to how custom apps and "agents" are governed. If your app is now classified as an "agent," new default policies may block it.
Check: Teams Admin Center → Permission policies — ensure the policy assigned to users still allows the custom app.
Setup Policy / Pinning Reset:
Microsoft occasionally resets or overrides setup policies during backend updates.
Check: Teams Admin Center → Setup policies — confirm the app is still pinned and the policy is still assigned to the correct users/groups.
"Agents" Settings:
You mentioned the app is being treated as an "agent." Microsoft has introduced new governance controls for agents in Teams.
If the admin disabled or restricted agents (e.g., via Teams Admin Center → Agents or Copilot settings), your app may be hidden as a side effect.
Check: Teams Admin Center → Agents — ensure custom agents/apps are not blocked.
App Availability:
Verify the app is still listed under Teams Admin Center → Manage apps and its status is "Allowed."
If the app was blocked or removed (even accidentally), it will vanish for all users.
Org-wide App Settings:
Check Teams Admin Center → Manage apps → Org-wide app settings.
Ensure "Allow interaction with custom apps" is enabled.

[benjaminyasoon]

Hi @Prasad-MSFT ,

thanks for your quick response!

One thing that I missed before: The app is visible in Outlook classic and OWA in the sidebar and can also be accessed via the office.com but not in Teams.

App Permission Policies Changed:
Microsoft has been rolling out changes to how custom apps and "agents" are governed. If your app is now classified as an "agent," new default policies may block it.
Check: Teams Admin Center → Permission policies — ensure the policy assigned to users still allows the custom app.

-> we checked that, looks good

Setup Policy / Pinning Reset:
Microsoft occasionally resets or overrides setup policies during backend updates.
Check: Teams Admin Center → Setup policies — confirm the app is still pinned and the policy is still assigned to the correct users/groups.

-> we checked that, looks good

"Agents" Settings:
You mentioned the app is being treated as an "agent." Microsoft has introduced new governance controls for agents in Teams.
If the admin disabled or restricted agents (e.g., via Teams Admin Center → Agents or Copilot settings), your app may be hidden as a side effect.
Check: Teams Admin Center → Agents — ensure custom agents/apps are not blocked.

-> we checked that setting within the Microsoft 365 admin center, I wasn't able to see an option in Teams Admin Center though.

App Availability:
Verify the app is still listed under Teams Admin Center → Manage apps and its status is "Allowed."
If the app was blocked or removed (even accidentally), it will vanish for all users.

-> we checked that, looks good

Org-wide App Settings:
Check Teams Admin Center → Manage apps → Org-wide app settings.
Ensure "Allow interaction with custom apps" is enabled.

-> we checked that setting and it worked before even though it is turned off, it is turned off for me too and the app works in my environment

Thank you!

[Prasad-MSFT]

Thank you for the detailed follow-up and for confirming the checks. Since the app is visible in Outlook but not in Teams, and all Teams Admin Center settings appear correct, here are some additional points and troubleshooting steps:

Microsoft has recently been converging Teams apps + Copilot agents + Outlook apps under a more unified model. If your app is now being treated as an agent, Teams may:

• Not show it in the left sidebar (like a normal Teams app)
• Only expose it via Copilot/agent entry points

Even if policies look correct, Teams may no longer render it as a pinnable app

What to verify:

1. In the manifest, check if anything recently changed (or was reprocessed by Microsoft):

• copilotExtensions
• webApplicationInfo
• or any new “agent” related schema

2. Check if the app still qualifies as a Teams “personal app”

If Teams doesn’t recognize it as a valid personal app anymore, it won’t appear in the sidebar.

• "staticTabs" (for personal app experience) still exists
• "scope": "personal" is present
• No schema validation warnings in Teams Admin Center

A silent schema validation failure can cause the app to:

Still exist in M365
But not render in Teams UI

[benjaminyasoon]

Hi @Prasad-MSFT ,
thanks for your help on this and your feedback! :)
Just to make it clearer: The App is not only NOT visible in the sidebar but also not visible in the Teams client anywhere (e.g. apps installed by your org).

We went through your bulletpoints and can confirm that we didn't change the following:

copilotExtensions
webApplicationInfo
or any new “agent” related schema

The app still qualifies as a Teams personal app.

Just another info: This app is a manifest file downloaded by the customer from our interface. They installed this manifest file a while ago. They didn't reuploaded it or anyting like that but the app disappeared. It can't be found in the app search bar in Teams.

I hope this helps! Would be happy to hear back from you! :)

Best regards,
Benjamin

[Prasad-MSFT]

thanks @benjaminyasoon for sharing these details. We have reached out to our engineering team to get their insights and guidance on this issue. We will keep you informed as soon as we receive an update or have more information to share.

Thank you for your understanding and patience.