M365 Copilot Agent Suddenly Stopped Retrieving Documents from SharePoint Knowledge Source

vinay G 5 Reputation points
2026-09-22T13:59:29.07+00:00

Hi Team, I have built an M365 Copilot Agent with a premium license. The agent uses a SharePoint document library as its knowledge source, which contains approximately 192,000 documents/items. The agent was created in January 2026 and had been working as expected for several months. It was successfully retrieving relevant documents based on the agent instructions and performing its tasks correctly. The agent was working correctly on September 7, 2026. However, starting on September 8, 2026, it suddenly stopped retrieving documents from the SharePoint knowledge source and is no longer able to complete its intended tasks. We have thoroughly checked the environment and are confident that:

  • No permissions were changed.
  • No SharePoint access settings were modified.
  • No changes were made to the knowledge source configuration.
  • No significant changes were made to the agent itself.

The solution was working correctly before and appears to have stopped working unexpectedly. Has anyone experienced a similar issue, or are there any known changes on the M365 Copilot side that could affect document retrieval from SharePoint knowledge sources? We have been unable to identify the root cause and would appreciate any guidance or recommendations for troubleshooting this issue.

Microsoft 365 and Office | SharePoint | Development

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  1. Kristen Tran 2,040 Reputation points Independent Advisor
    2026-09-22T15:15:45.42+00:00

    Hi vinay,

    Based on your findings, the behavior appears to be affecting multiple agents rather than a single agent configuration. The fact that the agents can identify a document when the exact file name is provided, but only return metadata (such as Created Date, Modified Date, and Author) instead of the document content, suggests that the file itself is still discoverable while content retrieval or grounding may not be functioning as expected. Copilot Studio relies on Microsoft Search indexing and content retrieval to generate responses from SharePoint knowledge sources.

    Reference: SharePoint Knowledge Sources Don't Return Results - Copilot Studio

    To help narrow down the root cause, I would recommend the following checks:

    1. Search for a unique phrase from within one of the affected documents directly in SharePoint (not just the file name) and confirm whether the document content is returned in SharePoint Search results.
    2. Using the same user account, test whether the document content can be retrieved through Microsoft 365 Copilot Chat.
      • If Copilot Chat is also unable to retrieve the content, this may indicate an indexing, permissions, or content-processing issue.
      • If Copilot Chat can retrieve the content successfully, the issue may be specific to the Copilot Agent knowledge source retrieval pipeline.
    3. Verify that the affected documents are not protected by encryption, sensitivity labels with encryption, Double Key Encryption (DKE), or password protection, as these can prevent Copilot from processing document contents even when the files remain accessible.
    4. Confirm with your SharePoint administrator whether Restricted SharePoint Search is enabled or if any related search settings have recently changed. This can impact SharePoint knowledge source retrieval.

    Given that:

    • The solution was working correctly through September 7, 2026,
    • The issue began suddenly on September 8, 2026,
    • Multiple existing and newly created agents are affected,
    • The same behavior occurs with smaller SharePoint knowledge sources,

    this may warrant further investigation by Microsoft Support to determine whether a service-side retrieval or indexing issue is involved.

    If possible, please share the results of the tests above, particularly whether the same content can be retrieved through Microsoft 365 Copilot Chat and SharePoint Search. Any screenshots, sample prompts, and correlation/conversation IDs would also be helpful for further analysis.

    I look forward to your update.

    Kind regards.

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  2. AI answer

    2026-09-22T13:59:51.02+00:00

    This pattern has been reported by others: previously working Copilot Studio agents stopped using SharePoint knowledge sources and started answering from general model knowledge instead. One documented case was later marked resolved after a service-side issue was addressed.

    For this scenario, the supported troubleshooting path is:

    1. Verify the affected user can open the exact SharePoint documents directly.
      • Copilot Studio respects Microsoft 365 security trimming.
      • If the user lacks read access, the agent returns no results and no explicit error.
    2. Test the same query with the same user account in Microsoft 365 Copilot Chat.
      • If Copilot Chat also cannot retrieve the content, that points to a permission or search indexing barrier.
    3. Check the SharePoint knowledge source authentication configuration.
      • For SharePoint knowledge sources configured with manual authentication, the Microsoft Entra ID app registration must include at least Sites.Read.All and Files.Read.All.
      • Those scopes must also be present in the agent authentication settings together with profile and openid.
      • Required consent must be granted.
      • If scopes are missing in either place, the agent can return no results without errors.
    4. Confirm Restricted SharePoint Search is not enabled for the tenant.
      • If it is enabled, SharePoint as a knowledge source is blocked regardless of app registration or agent configuration, and no results are returned.
      • If it is enabled, the relevant sites must be added to the allowed list.
    5. Validate indexing-related conditions.
      • If content is not indexed by Microsoft Search, retrieval can be incomplete or fail.
      • Recently added or changed content can require time to be indexed.
      • Inconsistent results can also occur while semantic index synchronization is still propagating.
    6. Verify the SharePoint path is still valid and accessible.
      • Invalid site or library paths can cause resource-not-found behavior.
    7. If using the SharePoint tool with agent APIs, confirm identity mode and tenant alignment.
      • The SharePoint tool requires user identity passthrough, not application-only authentication.
      • Cross-tenant access attempts can cause 401 or authentication failures.

    Based on the described timeline, there is no public documentation in the provided material describing a known Microsoft 365 Copilot platform change on September 8, 2026 that would intentionally disable SharePoint retrieval. The closest matching documented case indicates a service-side issue can cause this behavior even when existing and new agents are affected.

    A practical way to isolate the cause is:

    • test one known document path directly as the affected user,
    • run the same prompt in Microsoft 365 Copilot Chat with that same user,
    • review app registration and agent scopes,
    • confirm Restricted SharePoint Search status,
    • then wait/check for indexing propagation if content or search state recently changed.

    References:

    AI-generated content may be incorrect. Read our transparency notes for more information.

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