File Search citations are silently dropped on Gemini 3+ when the agent also has function tools

When Gemini's File Search tool was combined with at least one function tool on a Gemini 3+ model, the agent's file_search tool return had content None, so retrieved contexts and their custom_metadata (e.g. source_url) never reached the response. The API did return the grounding data; the framework skipped reconstructing it when explicit tool-invocation parts were present.

Framework / agent

Pydantic AI (pydantic-ai-slim) · Pydantic AI agent with native File Search plus function tools

Remediation attempts

TESTED

Recurrence

not documented

Source languages

en

Updated

2026-09-30

Sources

• GITHUB ISSUE Gemini File Search citations/grounding dropped on Gemini 3 when combined with function tools — github.com/pydantic/pydantic-ai, retrieved 2026-09-29
• GITHUB PULL REQUEST fix(google): recover Gemini 3+ File Search grounding dropped with native tool parts — github.com/pydantic/pydantic-ai, retrieved 2026-09-29

Symptoms

• The file_search NativeToolReturnPart content is None, so no citation or grounding metadata is recoverable from the response
• A raw SDK call with the same tool returns populated retrieved contexts including source_url

Similarity to your system is not implied. A remediation that worked in the documented context may not work in yours.