Copilot Studio

Copilot Studio Agent Returns MCS-1001 SystemError in Teams After Publishing Updates.

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Posted on by FC-01091015-0

Hi Community,

I am experiencing an issue with a Copilot Studio agent (New Experience) after publishing recent updates.

The agent was previously shared with multiple users and was working correctly in Microsoft Teams.

Recently, I updated the agent, including:

- Workflows

- Skills

- Knowledge sources

- Agent instructions

The agent published successfully without any errors.

However, after publishing, im getting the following error every time they interact with the agent from Microsoft Teams:

Sorry, an unexpected error occurred. Please try again, or contact your administrator with reference code MCS-1001 (conversation a:1GpPPhMDYTJ-sGWy0j8fD9_G5plZyGqUTA3B0tZgv-VxnR6Vz_AnGkYC0F9qYlUqce6otQKj1gLRcWTTvYiUFybiyajspBZ7BhcYuBWhQy6QtwF3mmFNUiqBue10icbx-).

(Error code: SystemError)

What makes this issue particularly strange is:

- The agent works correctly in the Copilot Studio Preview window.

- The agent works correctly in Microsoft 365 Copilot.

- New users can interact with the agent successfully from Teams.

- Only some existing users who had previously used the agent are affected.

Has anyone experienced a similar issue after publishing updates to an agent?

Thank you.

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Sam_Fawzi 1,150 Super User 2026 Season 1 on at

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Hey @FC-01091015-0,

The pattern you describe, working in the test pane, working in M365 Copilot, working for new Teams users, failing only for users who had used the agent before, points at Teams holding a cached version of the agent for those existing installs. This is documented as a configuration refresh issue on the Teams channel, where Teams keeps using a previously published version of the agent and surfaces a generic SystemError at runtime. Microsoft covers it under the SystemError after publishing or republishing section here: https://learn.microsoft.com/en-us/microsoft-copilot-studio/publication-add-bot-to-microsoft-teams#systemerror-after-publishing-or-republishing-an-agent

Two things to try, in order.

For the affected users, have them remove the agent app in Teams and re-add it. That clears the cached config and the persisted conversation state for that install. If a user cannot remove it, signing out of Teams and clearing the client cache has the same effect. This alone usually resolves it.

On your side, cycle the channel. In Copilot Studio turn off the Teams channel, save, turn it back on, then publish again. You can also disable and re-enable the agent app in the Teams admin center before republishing. That forces the newer version out to persistent channels.

One thing worth checking given what you changed. You added workflows and knowledge sources in this update. If any of those introduced a new connector or a new permission scope, existing users are running on a consent token issued before those scopes existed, while new users consent fresh on first use. That would produce exactly the split you are seeing. Have an affected user type sign out in the agent, then start a new conversation to force re-consent.

If it survives all of that, grab the conversation ID you posted along with the agent ID, environment, and timestamp, and raise a support ticket. SystemError persisting for multiple users after configuration is validated generally needs backend investigation.
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Mohsin Ali 1,075 on at

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Hello @FC-01091015-0 - For existing users, can you check with them reinstalling the agent after removing it once. It seems more like a configuration mismatching for them.
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M Bilal Khan 376 on at

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Hi @FC-01091015-0,
The pattern here points more toward a Teams-side conversation/session state issue than an issue with the agent itself.

Since the agent works in Copilot Studio Preview and Microsoft 365 Copilot, and new Teams users can use it successfully, while only existing users get MCS-1001, I would test the affected users’ Teams state first.

Try this with one affected user:

Sign out of Teams and sign back in.

Start a new chat/conversation with the agent rather than continuing the old conversation.

Remove the agent from Teams and add/reinstall it again.

Test in Teams web vs the Teams desktop client. If web works but desktop fails, that strongly points to cached client state.

If possible, test the same user from another device.

Check whether the issue disappears after reinstalling/re-adding the agent

Also check the agent's Teams channel configuration and publishing status after the latest update. Since the failure started immediately after publishing changes to workflows, skills, knowledge, and instructions, I'd also test by temporarily reverting the most recent change to identify whether a specific component is triggering the Teams error.

If the same affected users still receive MCS-1001 even after starting a fresh Teams conversation/reinstalling the agent, collect the conversation ID/reference code, affected user, timestamp, and Teams client type/version and raise it with Microsoft Support. The fact that new users work while existing users fail is an important clue for the investigation.

I wouldn't rebuild the agent yet—the current evidence suggests the published agent itself is functioning.