SharePoint knowledge source error "SubstrateSearch(NotFound)" / "NotFound in FederationWorkflow" in Copilot Studio agent

Question

SharePoint knowledge source error "SubstrateSearch(NotFound)" / "NotFound in FederationWorkflow" in Copilot Studio agent

Agente IA 5

We have a Copilot Studio agent connected to a SharePoint Online site as its knowledge source. Any query against this knowledge source fails consistently — including simple, generic queries with no specific target document.

Error shown in the UI:

"Something went wrong while searching this knowledge source."

Error details: Knowledge search · unknown

errorCode: SubstrateSearch(NotFound)

errorMessage: NotFound in FederationWorkflow

This happens for every query we try, including ones referencing documents we've confirmed exist and are indexed/accessible in the SharePoint site.

What we've already checked:

SharePoint site permissions (user has access)
Knowledge source connection status in Copilot Studio (shows as connected)
Removed and re-added the SharePoint knowledge source
Checked the exact document path/library (confirmed correct site URL, not a document library or folder link)
No sensitivity labels/IRM on the test documents

The failure is 100% consistent across different queries and different documents, which suggests the issue is with the federation/connection itself rather than specific content or permissions.

Has anyone seen this specific error code, and is there a known fix or workaround? Is this related to the SharePoint knowledge source issues reported in other threads (e.g., FederatedKnowledgeSearchOperation authentication prompts)?

Environment:

Copilot Studio agent with SharePoint Online as knowledge source
[agrega aquí: fecha aproximada en que empezó a fallar, y si hiciste algún cambio reciente de configuración]

Julio Fernández Fernández 0 Reputation points

2026-08-06T10:57:55.7733333+00:00

I'm experiencing the same issue in the classic experience since July 23 with a gradual progression in affected users in my tenant. Tried today the new copilot experience and I saw that's exactly the error I'm facing. Not public information from Microsoft available regarding to this problem.

2 answers

Your answer

Julio Fernández Fernández 0 Reputation points

2026-08-06T10:57:55.7733333+00:00

I'm experiencing the same issue in the classic experience since July 23 with a gradual progression in affected users in my tenant. Tried today the new copilot experience and I saw that's exactly the error I'm facing. Not public information from Microsoft available regarding to this problem.

Answer 1

That error code isn't in the official docs — it's a hard failure at the federation layer, not the usual "silent no-results" case. Since it fails on every query regardless of content, most likely causes, in order:

Auth mode vs. Tenant graph grounding mismatch — the semantic-index search path needs "Authenticate with Microsoft." If you're on manual auth with that setting on (or mismatched), federation fails outright. Check Settings → Generative AI vs. Settings → Security → Authentication.
Missing Graph scopes (manual auth only) — confirm Sites.Read.All and Files.Read.All are granted and consented on the app registration.
Restricted SharePoint Search enabled tenant-wide — blocks federation regardless of agent config. Check with your SharePoint admin.
Stale source link — if the site was renamed/moved, remove the source and re-add using a fresh URL.
Possible backend issue — there's a currently open, Microsoft-acknowledged issue with SharePoint knowledge source federation/auth failures (raised via ICM, no public advisory number published). If none of the above fixes it, worth opening a ticket with the exact timestamp and conversation ID.
https://community.powerplatform.com/forums/thread/details/?threadid=4cacf705-5c37-f111-88b5-000d3a54c279

Can you confirm: Authenticate with Microsoft or manual? Tenant graph grounding on/off? And roughly when this started?

Julio Fernández Fernández 0 Reputation points

2026-08-19T08:08:48.26+00:00

In my case none of the above worked. We have opened a ticket with the details. I see more people affected by the same problem in similar threads.

Answer 2

Hi Agente IA

I looked into the error codes SubstrateSearch(NotFound) and NotFound in FederationWorkflow, but I couldn't find any official documentation, public information, or known workaround for this specific issue.

As you've already gone through the common troubleshooting steps, I recommend contacting Microsoft Support so they can investigate this issue further.

You can create a support request by following these steps:

Sign in to the Microsoft 365 admin center using your Microsoft 365 Business administrator account.
Select the Help & support (headset) icon.
If Support Assistant is enabled, turn it off.
Type contact support in the search box.
Select Contact support, then choose Phone or Email to submit your request.

For further instructions, you can follow this guide: Get support - Microsoft 365 admin | Microsoft Learn.

Please note that we are not Microsoft Support. This is a user-to-user community forum, and moderators here do not have access to your environment or Microsoft's backend systems. We can only provide guidance based on publicly available information and community experience.

I appreciate your understanding, and I hope your issue will be resolved soon.

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