diff --git a/src/core/assistant-message/presentAssistantMessage.ts b/src/core/assistant-message/presentAssistantMessage.ts
index ee3fa148b4..55aba57a92 100644
--- a/src/core/assistant-message/presentAssistantMessage.ts
+++ b/src/core/assistant-message/presentAssistantMessage.ts
@@ -527,13 +527,9 @@ export async function presentAssistantMessage(cline: Task) {
 			break
 	}
 
-	const recentlyModifiedFiles = cline.fileContextTracker.getAndClearCheckpointPossibleFile()
-
-	if (recentlyModifiedFiles.length > 0) {
-		// TODO: We can track what file changes were made and only
-		// checkpoint those files, this will be save storage.
-		await checkpointSave(cline)
-	}
+	// Save checkpoint after every message, not just when files are modified
+	// This ensures user's manual edits between messages are preserved
+	await checkpointSave(cline)
 
 	// Seeing out of bounds is fine, it means that the next too call is being
 	// built up and ready to add to assistantMessageContent to present.
diff --git a/src/core/task/Task.ts b/src/core/task/Task.ts
index 53b8ef5b87..fb30dc1ef3 100644
--- a/src/core/task/Task.ts
+++ b/src/core/task/Task.ts
@@ -1245,6 +1245,9 @@ export class Task extends EventEmitter<ClineEvents> {
 		await this.addToApiConversationHistory({ role: "user", content: finalUserContent })
 		TelemetryService.instance.captureConversationMessage(this.taskId, "user")
 
+		// Save checkpoint after user message to preserve any manual edits
+		await checkpointSave(this)
+
 		// Since we sent off a placeholder api_req_started message to update the
 		// webview while waiting to actually start the API request (to load
 		// potential details for example), we need to update the text of that