diff --git a/packages/pi-agent-core/src/agent.ts b/packages/pi-agent-core/src/agent.ts
index 14a0a33ac..112573650 100644
--- a/packages/pi-agent-core/src/agent.ts
+++ b/packages/pi-agent-core/src/agent.ts
@@ -103,6 +103,15 @@ export interface AgentOptions {
 	maxRetryDelayMs?: number;
 }
 
+/**
+ * Internal wrapper that tracks message origin for origin-aware queue clearing.
+ * "user" = typed by human in TUI; "system" = generated by extensions/background jobs.
+ */
+interface QueueEntry {
+	message: AgentMessage;
+	origin: "user" | "system";
+}
+
 export class Agent {
 	private _state: AgentState = {
 		systemPrompt: "",
@@ -120,8 +129,8 @@ export class Agent {
 	private abortController?: AbortController;
 	private convertToLlm: (messages: AgentMessage[]) => Message[] | Promise<Message[]>;
 	private transformContext?: (messages: AgentMessage[], signal?: AbortSignal) => Promise<AgentMessage[]>;
-	private steeringQueue: AgentMessage[] = [];
-	private followUpQueue: AgentMessage[] = [];
+	private steeringQueue: QueueEntry[] = [];
+	private followUpQueue: QueueEntry[] = [];
 	private steeringMode: "all" | "one-at-a-time";
 	private followUpMode: "all" | "one-at-a-time";
 	public streamFn: StreamFn;
@@ -279,16 +288,16 @@ export class Agent {
 	 * Queue a steering message to interrupt the agent mid-run.
 	 * Delivered after current tool execution, skips remaining tools.
 	 */
-	steer(m: AgentMessage) {
-		this.steeringQueue.push(m);
+	steer(m: AgentMessage, origin: "user" | "system" = "system") {
+		this.steeringQueue.push({ message: m, origin });
 	}
 
 	/**
 	 * Queue a follow-up message to be processed after the agent finishes.
 	 * Delivered only when agent has no more tool calls or steering messages.
 	 */
-	followUp(m: AgentMessage) {
-		this.followUpQueue.push(m);
+	followUp(m: AgentMessage, origin: "user" | "system" = "system") {
+		this.followUpQueue.push({ message: m, origin });
 	}
 
 	clearSteeringQueue() {
@@ -304,6 +313,18 @@ export class Agent {
 		this.followUpQueue = [];
 	}
 
+	/**
+	 * Drain user-origin messages from queues, leaving system messages in place.
+	 * Used during abort to preserve messages the user explicitly typed.
+	 */
+	drainUserMessages(): { steering: AgentMessage[]; followUp: AgentMessage[] } {
+		const userSteering = this.steeringQueue.filter((e) => e.origin === "user").map((e) => e.message);
+		const userFollowUp = this.followUpQueue.filter((e) => e.origin === "user").map((e) => e.message);
+		this.steeringQueue = this.steeringQueue.filter((e) => e.origin !== "user");
+		this.followUpQueue = this.followUpQueue.filter((e) => e.origin !== "user");
+		return { steering: userSteering, followUp: userFollowUp };
+	}
+
 	hasQueuedMessages(): boolean {
 		return this.steeringQueue.length > 0 || this.followUpQueue.length > 0;
 	}
@@ -313,12 +334,12 @@ export class Agent {
 			if (this.steeringQueue.length > 0) {
 				const first = this.steeringQueue[0];
 				this.steeringQueue = this.steeringQueue.slice(1);
-				return [first];
+				return [first.message];
 			}
 			return [];
 		}
 
-		const steering = this.steeringQueue.slice();
+		const steering = this.steeringQueue.map((e) => e.message);
 		this.steeringQueue = [];
 		return steering;
 	}
@@ -328,12 +349,12 @@ export class Agent {
 			if (this.followUpQueue.length > 0) {
 				const first = this.followUpQueue[0];
 				this.followUpQueue = this.followUpQueue.slice(1);
-				return [first];
+				return [first.message];
 			}
 			return [];
 		}
 
-		const followUp = this.followUpQueue.slice();
+		const followUp = this.followUpQueue.map((e) => e.message);
 		this.followUpQueue = [];
 		return followUp;
 	}
diff --git a/packages/pi-coding-agent/src/core/agent-session.ts b/packages/pi-coding-agent/src/core/agent-session.ts
index d09946b39..acd234702 100644
--- a/packages/pi-coding-agent/src/core/agent-session.ts
+++ b/packages/pi-coding-agent/src/core/agent-session.ts
@@ -1171,11 +1171,14 @@ export class AgentSession {
 		if (images) {
 			content.push(...images);
 		}
-		this.agent.steer({
-			role: "user",
-			content,
-			timestamp: Date.now(),
-		});
+		this.agent.steer(
+			{
+				role: "user",
+				content,
+				timestamp: Date.now(),
+			},
+			"user",
+		);
 	}
 
 	/**
@@ -1187,11 +1190,14 @@ export class AgentSession {
 		if (images) {
 			content.push(...images);
 		}
-		this.agent.followUp({
-			role: "user",
-			content,
-			timestamp: Date.now(),
-		});
+		this.agent.followUp(
+			{
+				role: "user",
+				content,
+				timestamp: Date.now(),
+			},
+			"user",
+		);
 	}
 
 	/**
@@ -1304,10 +1310,28 @@ export class AgentSession {
 	 * @returns Object with steering and followUp arrays
 	 */
 	clearQueue(): { steering: string[]; followUp: string[] } {
-		const steering = [...this._steeringMessages];
-		const followUp = [...this._followUpMessages];
+		// Drain user-origin messages from agent queues before clearing.
+		// This preserves messages the user explicitly typed during streaming,
+		// while system-generated messages (extension notifications, etc.) are discarded.
+		const userMessages = this.agent.drainUserMessages();
+
+		// Extract text content from preserved user messages
+		const extractText = (m: AgentMessage): string => {
+			if (!("content" in m) || !Array.isArray(m.content)) return "";
+			const textPart = m.content.find((c: { type: string }) => c.type === "text");
+			return textPart && "text" in textPart ? (textPart as { text: string }).text : "";
+		};
+		const preservedSteering = userMessages.steering.map(extractText).filter((t) => t.length > 0);
+		const preservedFollowUp = userMessages.followUp.map(extractText).filter((t) => t.length > 0);
+
+		// Session-level string arrays track what was queued for display purposes.
+		// Return the full set (session-tracked + any agent-only user messages).
+		const steering = [...this._steeringMessages, ...preservedSteering];
+		const followUp = [...this._followUpMessages, ...preservedFollowUp];
 		this._steeringMessages = [];
 		this._followUpMessages = [];
+
+		// Clear remaining system messages from agent queues
 		this.agent.clearAllQueues();
 		return { steering, followUp };
 	}