diff --git a/extensions/copilot/src/platform/endpoint/node/chatEndpoint.ts b/extensions/copilot/src/platform/endpoint/node/chatEndpoint.ts
index 7ee7bf18123..a1c499abae0 100644
--- a/extensions/copilot/src/platform/endpoint/node/chatEndpoint.ts
+++ b/extensions/copilot/src/platform/endpoint/node/chatEndpoint.ts
@@ -316,6 +316,20 @@ export class ChatEndpoint implements IChatEndpoint {
 				body.thinking_budget = thinkingBudget;
 			}
 		}
+
+		// Apply Gemini function calling mode if configured
+		const hasTools = !!options.requestOptions?.tools?.length;
+		if (hasTools && this.family.toLowerCase().includes('gemini-3')) {
+			const geminiFunctionCallingMode = this._configurationService.getExperimentBasedConfig(
+				ConfigKey.TeamInternal.GeminiFunctionCallingMode,
+				this._expService
+			);
+			// Only override tool_choice if experiment provides a value and user hasn't specified a function call
+			if (geminiFunctionCallingMode && typeof body.tool_choice !== 'object') {
+				body.tool_choice = geminiFunctionCallingMode;
+			}
+		}
+
 		return body;
 	}
 
diff --git a/extensions/copilot/src/platform/endpoint/node/responsesApi.ts b/extensions/copilot/src/platform/endpoint/node/responsesApi.ts
index 512a326b4a8..5d32b8e074b 100644
--- a/extensions/copilot/src/platform/endpoint/node/responsesApi.ts
+++ b/extensions/copilot/src/platform/endpoint/node/responsesApi.ts
@@ -32,11 +32,6 @@ export function createResponsesRequestBody(accessor: ServicesAccessor, options:
 	const expService = accessor.get(IExperimentationService);
 	const verbosity = getVerbosityForModelSync(endpoint);
 
-	const hasTools = !!options.requestOptions?.tools?.length;
-	const geminiFunctionCallingMode = hasTools && endpoint.family.toLowerCase().includes('gemini-3')
-		? configService.getExperimentBasedConfig(ConfigKey.TeamInternal.GeminiFunctionCallingMode, expService)
-		: undefined;
-
 	const body: IEndpointBody = {
 		model,
 		...rawMessagesToResponseAPI(model, options.messages, !!options.ignoreStatefulMarker),
@@ -50,11 +45,9 @@ export function createResponsesRequestBody(accessor: ServicesAccessor, options:
 		// Only a subset of completion post options are supported, and some
 		// are renamed. Handle them manually:
 		max_output_tokens: options.postOptions.max_tokens,
-		tool_choice: geminiFunctionCallingMode && typeof options.postOptions.tool_choice !== 'object'
-			? geminiFunctionCallingMode
-			: (typeof options.postOptions.tool_choice === 'object'
-				? { type: 'function', name: options.postOptions.tool_choice.function.name }
-				: options.postOptions.tool_choice),
+		tool_choice: typeof options.postOptions.tool_choice === 'object'
+			? { type: 'function', name: options.postOptions.tool_choice.function.name }
+			: options.postOptions.tool_choice,
 		top_logprobs: options.postOptions.logprobs ? 3 : undefined,
 		store: false,
 		text: verbosity ? { verbosity } : undefined,