diff --git a/src/core/task/Task.ts b/src/core/task/Task.ts
index e7104d1832..bf94f40a0d 100644
--- a/src/core/task/Task.ts
+++ b/src/core/task/Task.ts
@@ -866,9 +866,18 @@ export class Task extends EventEmitter<TaskEvents> implements TaskLike {
 
 		// Validate and fix tool_result IDs against the previous assistant message
 		const validatedMessage = validateAndFixToolResultIds(userMessage, this.apiConversationHistory)
-		const userMessageWithTs = { ...validatedMessage, ts: Date.now() }
+		// Use pendingUserMessageTs if set (for file context tracking coordination)
+		// This ensures the message timestamp matches what was set during tool execution
+		const messageTs = this.pendingUserMessageTs ?? Date.now()
+		const userMessageWithTs = { ...validatedMessage, ts: messageTs }
 		this.apiConversationHistory.push(userMessageWithTs as ApiMessage)
 
+		// Clear the pending timestamp and message context after use
+		if (this.pendingUserMessageTs) {
+			this.pendingUserMessageTs = null
+			this.fileContextTracker.clearCurrentMessageContext()
+		}
+
 		await this.saveApiConversationHistory()
 
 		// Clear the pending content since it's now saved
diff --git a/webview-ui/src/context/__tests__/ExtensionStateContext.spec.tsx b/webview-ui/src/context/__tests__/ExtensionStateContext.spec.tsx
index 15c87d03c4..c3dfe3796e 100644
--- a/webview-ui/src/context/__tests__/ExtensionStateContext.spec.tsx
+++ b/webview-ui/src/context/__tests__/ExtensionStateContext.spec.tsx
@@ -240,6 +240,7 @@ describe("mergeExtensionState", () => {
 				runSlashCommand: false,
 				nativeToolCalling: false,
 				multipleNativeToolCalls: false,
+				smartContextTracking: false,
 			} as Record<ExperimentId, boolean>,
 			checkpointTimeout: DEFAULT_CHECKPOINT_TIMEOUT_SECONDS + 5,
 		}
@@ -263,6 +264,7 @@ describe("mergeExtensionState", () => {
 			runSlashCommand: false,
 			nativeToolCalling: false,
 			multipleNativeToolCalls: false,
+			smartContextTracking: false,
 		})
 	})
 })