diff --git a/apps/cli/src/agent/__tests__/json-event-emitter-streaming.test.ts b/apps/cli/src/agent/__tests__/json-event-emitter-streaming.test.ts
index 329e06d24a0..d80e66ceb55 100644
--- a/apps/cli/src/agent/__tests__/json-event-emitter-streaming.test.ts
+++ b/apps/cli/src/agent/__tests__/json-event-emitter-streaming.test.ts
@@ -215,4 +215,132 @@ describe("JsonEventEmitter streaming deltas", () => {
 		expect(output[0]).toMatchObject({ content: "gh" })
 		expect(output[1]).toMatchObject({ content: " pr" })
 	})
+
+	it("streams say:command_output as deltas and correlates tool_result id to execute_command", () => {
+		const { stdout, lines } = createMockStdout()
+		const emitter = new JsonEventEmitter({ mode: "stream-json", stdout })
+		const commandId = 404
+		const outputTs = 405
+
+		emitMessage(
+			emitter,
+			createAskMessage({
+				ts: commandId,
+				ask: "command",
+				partial: false,
+				text: "echo hello",
+			}),
+		)
+
+		emitMessage(emitter, {
+			ts: outputTs,
+			type: "say",
+			say: "command_output",
+			partial: true,
+			text: "line1\n",
+		} as ClineMessage)
+		emitMessage(emitter, {
+			ts: outputTs,
+			type: "say",
+			say: "command_output",
+			partial: true,
+			text: "line1\nline2\n",
+		} as ClineMessage)
+		emitMessage(emitter, {
+			ts: outputTs,
+			type: "say",
+			say: "command_output",
+			partial: false,
+			text: "line1\nline2\n",
+		} as ClineMessage)
+
+		const output = lines()
+		expect(output).toHaveLength(4)
+		expect(output[0]).toMatchObject({
+			type: "tool_use",
+			id: commandId,
+			subtype: "command",
+			tool_use: { name: "execute_command", input: { command: "echo hello" } },
+			done: true,
+		})
+		expect(output[1]).toMatchObject({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command", output: "line1\n" },
+		})
+		expect(output[2]).toMatchObject({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command", output: "line2\n" },
+		})
+		expect(output[3]).toMatchObject({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command" },
+			done: true,
+		})
+		expect(output[3]).not.toHaveProperty("tool_result.output")
+	})
+
+	it("prefers status-driven command output streaming and suppresses duplicate say completion", () => {
+		const { stdout, lines } = createMockStdout()
+		const emitter = new JsonEventEmitter({ mode: "stream-json", stdout })
+		const commandId = 505
+
+		emitMessage(
+			emitter,
+			createAskMessage({
+				ts: commandId,
+				ask: "command",
+				partial: false,
+				text: "echo streamed",
+			}),
+		)
+
+		emitter.emitCommandOutputChunk("line1\n")
+		emitter.emitCommandOutputChunk("line1\nline2\n")
+		emitter.emitCommandOutputDone()
+
+		// This completion say is expected from the extension, but should be suppressed
+		// because we already streamed and completed via commandExecutionStatus.
+		emitMessage(emitter, {
+			ts: 999,
+			type: "say",
+			say: "command_output",
+			partial: false,
+			text: "line1\nline2\n",
+		} as ClineMessage)
+
+		const output = lines()
+		expect(output).toHaveLength(4)
+		expect(output[0]).toMatchObject({
+			type: "tool_use",
+			id: commandId,
+			subtype: "command",
+			tool_use: { name: "execute_command", input: { command: "echo streamed" } },
+			done: true,
+		})
+		expect(output[1]).toMatchObject({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command", output: "line1\n" },
+		})
+		expect(output[2]).toMatchObject({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command", output: "line2\n" },
+		})
+		expect(output[3]).toMatchObject({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command" },
+			done: true,
+		})
+	})
 })
diff --git a/apps/cli/src/agent/json-event-emitter.ts b/apps/cli/src/agent/json-event-emitter.ts
index f46c39be506..e0f5d5bea64 100644
--- a/apps/cli/src/agent/json-event-emitter.ts
+++ b/apps/cli/src/agent/json-event-emitter.ts
@@ -107,6 +107,16 @@ export class JsonEventEmitter {
 	private previousContent = new Map<number, string>()
 	// Track previous tool-use content for structured (non-append-only) delta computation.
 	private previousToolUseContent = new Map<number, string>()
+	// Track the currently active execute_command tool_use id for command_output correlation.
+	private activeCommandToolUseId: number | undefined
+	// Track command output snapshots by command tool-use id for delta computation.
+	private previousCommandOutputByToolUseId = new Map<number, string>()
+	// Track command ids whose output is being streamed from commandExecutionStatus updates.
+	private statusDrivenCommandOutputIds = new Set<number>()
+	// Track command ids that already emitted a terminal command_output done event.
+	private completedCommandOutputIds = new Set<number>()
+	// Suppress the next say:command_output completion message after status-driven streaming.
+	private suppressNextCommandOutputSay = false
 	// Track the completion result content
 	private completionResultContent: string | undefined
 	// Track the latest assistant text as a fallback for result.content.
@@ -288,6 +298,90 @@ export class JsonEventEmitter {
 		return this.mode === "stream-json" && content === null
 	}
 
+	private computeCommandOutputDelta(commandId: number, fullOutput: string | undefined): string | null {
+		const normalized = fullOutput ?? ""
+		const previous = this.previousCommandOutputByToolUseId.get(commandId) || ""
+
+		if (normalized === previous) {
+			return null
+		}
+
+		this.previousCommandOutputByToolUseId.set(commandId, normalized)
+		return normalized.startsWith(previous) ? normalized.slice(previous.length) : normalized
+	}
+
+	private emitCommandOutputEvent(commandId: number, fullOutput: string | undefined, isDone: boolean): void {
+		if (this.mode === "stream-json") {
+			const outputDelta = this.computeCommandOutputDelta(commandId, fullOutput)
+			const event: JsonEvent = {
+				type: "tool_result",
+				id: commandId,
+				subtype: "command",
+				tool_result: { name: "execute_command" },
+			}
+
+			if (outputDelta !== null && outputDelta.length > 0) {
+				event.tool_result = { name: "execute_command", output: outputDelta }
+			}
+
+			if (isDone) {
+				event.done = true
+				this.previousCommandOutputByToolUseId.delete(commandId)
+				this.statusDrivenCommandOutputIds.delete(commandId)
+				this.completedCommandOutputIds.add(commandId)
+				if (this.activeCommandToolUseId === commandId) {
+					this.activeCommandToolUseId = undefined
+				}
+			}
+
+			// Suppress empty partial updates that carry no delta.
+			if (!isDone && outputDelta === null) {
+				return
+			}
+
+			this.emitEvent(event)
+			return
+		}
+
+		this.emitEvent({
+			type: "tool_result",
+			id: commandId,
+			subtype: "command",
+			tool_result: { name: "execute_command", output: fullOutput },
+			...(isDone ? { done: true } : {}),
+		})
+
+		if (isDone) {
+			this.previousCommandOutputByToolUseId.delete(commandId)
+			this.statusDrivenCommandOutputIds.delete(commandId)
+			this.completedCommandOutputIds.add(commandId)
+			if (this.activeCommandToolUseId === commandId) {
+				this.activeCommandToolUseId = undefined
+			}
+		}
+	}
+
+	public emitCommandOutputChunk(outputSnapshot: string): void {
+		const commandId = this.activeCommandToolUseId
+		if (commandId === undefined) {
+			return
+		}
+
+		this.statusDrivenCommandOutputIds.add(commandId)
+		this.emitCommandOutputEvent(commandId, outputSnapshot, false)
+	}
+
+	public emitCommandOutputDone(): void {
+		const commandId = this.activeCommandToolUseId
+		if (commandId === undefined) {
+			return
+		}
+
+		this.statusDrivenCommandOutputIds.add(commandId)
+		this.suppressNextCommandOutputSay = true
+		this.emitCommandOutputEvent(commandId, undefined, true)
+	}
+
 	/**
 	 * Get content to send for a message (delta for streaming, full for json mode).
 	 */
@@ -392,10 +486,7 @@ export class JsonEventEmitter {
 				break
 
 			case "command_output":
-				this.emitEvent({
-					type: "tool_result",
-					tool_result: { name: "execute_command", output: msg.text },
-				})
+				this.handleCommandOutputMessage(msg, isDone)
 				break
 
 			case "user_feedback":
@@ -517,6 +608,10 @@ export class JsonEventEmitter {
 		const toolInfo = parseToolInfo(msg.text)
 
 		if (subtype === "command") {
+			this.activeCommandToolUseId = msg.ts
+			this.completedCommandOutputIds.delete(msg.ts)
+			this.suppressNextCommandOutputSay = false
+
 			if (isStreamingPartial) {
 				const commandDelta = this.computeStructuredDelta(msg.ts, msg.text)
 				if (commandDelta === null) {
@@ -595,6 +690,21 @@ export class JsonEventEmitter {
 		})
 	}
 
+	private handleCommandOutputMessage(msg: ClineMessage, isDone: boolean): void {
+		if (this.suppressNextCommandOutputSay) {
+			if (isDone) {
+				this.suppressNextCommandOutputSay = false
+			}
+			return
+		}
+
+		const commandId = this.activeCommandToolUseId ?? msg.ts
+		if (this.statusDrivenCommandOutputIds.has(commandId) || this.completedCommandOutputIds.has(commandId)) {
+			return
+		}
+		this.emitCommandOutputEvent(commandId, msg.text, isDone)
+	}
+
 	/**
 	 * Handle task completion and emit result event.
 	 */
@@ -711,6 +821,11 @@ export class JsonEventEmitter {
 		this.seenMessageIds.clear()
 		this.previousContent.clear()
 		this.previousToolUseContent.clear()
+		this.activeCommandToolUseId = undefined
+		this.previousCommandOutputByToolUseId.clear()
+		this.statusDrivenCommandOutputIds.clear()
+		this.completedCommandOutputIds.clear()
+		this.suppressNextCommandOutputSay = false
 		this.completionResultContent = undefined
 		this.lastAssistantText = undefined
 		this.expectPromptEchoAsUser = true
diff --git a/apps/cli/src/commands/cli/stdin-stream.ts b/apps/cli/src/commands/cli/stdin-stream.ts
index 9ad89ef1c7d..318328a3961 100644
--- a/apps/cli/src/commands/cli/stdin-stream.ts
+++ b/apps/cli/src/commands/cli/stdin-stream.ts
@@ -349,12 +349,46 @@ export async function runStdinStreamMode({ host, jsonEmitter, setStreamRequestId
 
 	const onExtensionMessage = (message: {
 		type?: string
+		text?: unknown
 		state?: {
 			currentTaskId?: unknown
 			currentTaskItem?: { id?: unknown }
 			messageQueue?: unknown
 		}
 	}) => {
+		if (message.type === "commandExecutionStatus") {
+			if (typeof message.text !== "string") {
+				return
+			}
+
+			let parsedStatus: unknown
+			try {
+				parsedStatus = JSON.parse(message.text)
+			} catch {
+				return
+			}
+
+			if (!isRecord(parsedStatus) || typeof parsedStatus.status !== "string") {
+				return
+			}
+
+			if (parsedStatus.status === "output" && typeof parsedStatus.output === "string") {
+				jsonEmitter.emitCommandOutputChunk(parsedStatus.output)
+				return
+			}
+
+			if (
+				parsedStatus.status === "exited" ||
+				parsedStatus.status === "timeout" ||
+				parsedStatus.status === "fallback"
+			) {
+				jsonEmitter.emitCommandOutputDone()
+				return
+			}
+
+			return
+		}
+
 		if (message.type !== "state") {
 			return
 		}
@@ -463,7 +497,7 @@ export async function runStdinStreamMode({ host, jsonEmitter, setStreamRequestId
 			}
 
 			switch (stdinCommand.command) {
-				case "start":
+				case "start": {
 					// A task can emit completion events before runTask() finalizers run.
 					// Wait for full settlement to avoid false "task_busy" on immediate next start.
 					// Safe from races: `for await` processes stdin commands serially, so no
@@ -503,8 +537,16 @@ export async function runStdinStreamMode({ host, jsonEmitter, setStreamRequestId
 						success: true,
 					})
 
+					// In CLI stdin-stream mode, default to the execa terminal provider so
+					// command output can be streamed deterministically. Explicit per-request
+					// config still wins.
+					const taskConfiguration = {
+						terminalShellIntegrationDisabled: true,
+						...(stdinCommand.configuration ?? {}),
+					}
+
 					activeTaskPromise = host
-						.runTask(stdinCommand.prompt, latestTaskId, stdinCommand.configuration)
+						.runTask(stdinCommand.prompt, latestTaskId, taskConfiguration)
 						.catch((error) => {
 							const message = error instanceof Error ? error.message : String(error)
 
@@ -559,6 +601,7 @@ export async function runStdinStreamMode({ host, jsonEmitter, setStreamRequestId
 						})
 
 					break
+				}
 
 				case "message": {
 					// If cancel was requested, wait briefly for the task to be rehydrated
diff --git a/src/core/task/Task.ts b/src/core/task/Task.ts
index 1d4320493a0..4f8a5e49fdc 100644
--- a/src/core/task/Task.ts
+++ b/src/core/task/Task.ts
@@ -1383,6 +1383,9 @@ export class Task extends EventEmitter<TaskEvents> implements TaskLike {
 		// block (via the `pWaitFor`).
 		const isBlocking = !(this.askResponse !== undefined || this.lastMessageTs !== askTs)
 		const isMessageQueued = !this.messageQueueService.isEmpty()
+		// Keep queued user messages intact during command_output asks. Those asks
+		// are terminal flow-control, not conversational turns.
+		const shouldDrainQueuedMessageForAsk = type !== "command_output"
 		const isStatusMutable = !partial && isBlocking && !isMessageQueued && approval.decision === "ask"
 
 		if (isStatusMutable) {
@@ -1423,7 +1426,7 @@ export class Task extends EventEmitter<TaskEvents> implements TaskLike {
 					}, statusMutationTimeout),
 				)
 			}
-		} else if (isMessageQueued) {
+		} else if (isMessageQueued && shouldDrainQueuedMessageForAsk) {
 			const message = this.messageQueueService.dequeueMessage()
 
 			if (message) {
@@ -1450,7 +1453,7 @@ export class Task extends EventEmitter<TaskEvents> implements TaskLike {
 				// If a queued message arrives while we're blocked on an ask (e.g. a follow-up
 				// suggestion click that was incorrectly queued due to UI state), consume it
 				// immediately so the task doesn't hang.
-				if (!this.messageQueueService.isEmpty()) {
+				if (shouldDrainQueuedMessageForAsk && !this.messageQueueService.isEmpty()) {
 					const message = this.messageQueueService.dequeueMessage()
 					if (message) {
 						// If this is a tool approval ask, we need to approve first (yesButtonClicked)
diff --git a/src/core/task/__tests__/ask-queued-message-drain.spec.ts b/src/core/task/__tests__/ask-queued-message-drain.spec.ts
index 3b4097a9407..06f577881ec 100644
--- a/src/core/task/__tests__/ask-queued-message-drain.spec.ts
+++ b/src/core/task/__tests__/ask-queued-message-drain.spec.ts
@@ -35,4 +35,38 @@ describe("Task.ask queued message drain", () => {
 		expect(result.response).toBe("messageResponse")
 		expect(result.text).toBe("picked answer")
 	})
+
+	it("does not consume queued messages for command_output asks", async () => {
+		const task = Object.create(Task.prototype) as Task
+		;(task as any).abort = false
+		;(task as any).clineMessages = []
+		;(task as any).askResponse = undefined
+		;(task as any).askResponseText = undefined
+		;(task as any).askResponseImages = undefined
+		;(task as any).lastMessageTs = undefined
+
+		const { MessageQueueService } = await import("../../message-queue/MessageQueueService")
+		;(task as any).messageQueueService = new MessageQueueService()
+		;(task as any).addToClineMessages = vi.fn(async () => {})
+		;(task as any).saveClineMessages = vi.fn(async () => {})
+		;(task as any).updateClineMessage = vi.fn(async () => {})
+		;(task as any).cancelAutoApprovalTimeout = vi.fn(() => {})
+		;(task as any).checkpointSave = vi.fn(async () => {})
+		;(task as any).emit = vi.fn()
+		;(task as any).providerRef = { deref: () => undefined }
+
+		const askPromise = task.ask("command_output", "command is still running...", false)
+		;(task as any).messageQueueService.addMessage("1+1=?")
+
+		setTimeout(() => {
+			task.approveAsk()
+		}, 0)
+
+		const result = await askPromise
+
+		expect(result.response).toBe("yesButtonClicked")
+		expect(result.text).toBeUndefined()
+		expect((task as any).messageQueueService.isEmpty()).toBe(false)
+		expect((task as any).messageQueueService.messages[0]?.text).toBe("1+1=?")
+	})
 })
diff --git a/src/core/tools/ExecuteCommandTool.ts b/src/core/tools/ExecuteCommandTool.ts
index cb6fc6ff023..7d690d67ddd 100644
--- a/src/core/tools/ExecuteCommandTool.ts
+++ b/src/core/tools/ExecuteCommandTool.ts
@@ -218,6 +218,53 @@ export async function executeCommandInTerminal(
 	// Bound accumulated output buffer size to prevent unbounded memory growth for long-running commands.
 	// The interceptor preserves full output; this buffer is only for UI display (100KB limit).
 	const maxAccumulatedOutputSize = 100_000
+	const commandOutputStreamThrottleMs = 150
+	let latestCompressedOutput = ""
+	let lastQueuedCommandOutput = ""
+	let lastCommandOutputEmitAt = 0
+	let pendingCommandOutputEmitTimer: NodeJS.Timeout | undefined
+	let commandOutputSayChain: Promise<void> = Promise.resolve()
+
+	const queueCommandOutputMessage = (text: string, partial: boolean, force = false): Promise<void> => {
+		if (!force && text === lastQueuedCommandOutput) {
+			return commandOutputSayChain
+		}
+
+		lastQueuedCommandOutput = text
+		commandOutputSayChain = commandOutputSayChain
+			.then(async () => {
+				await task.say("command_output", text, undefined, partial, undefined, undefined, {
+					isNonInteractive: true,
+				})
+			})
+			.catch((error) => {
+				console.error("[ExecuteCommandTool] Failed to publish command output:", error)
+			})
+
+		return commandOutputSayChain
+	}
+
+	const schedulePartialCommandOutputUpdate = () => {
+		if (!latestCompressedOutput || completed) {
+			return
+		}
+
+		const emitUpdate = () => {
+			pendingCommandOutputEmitTimer = undefined
+			lastCommandOutputEmitAt = Date.now()
+			void queueCommandOutputMessage(latestCompressedOutput, true)
+		}
+
+		const elapsed = Date.now() - lastCommandOutputEmitAt
+		if (elapsed >= commandOutputStreamThrottleMs) {
+			emitUpdate()
+			return
+		}
+
+		if (!pendingCommandOutputEmitTimer) {
+			pendingCommandOutputEmitTimer = setTimeout(emitUpdate, commandOutputStreamThrottleMs - elapsed)
+		}
+	}
 
 	// Track when onCompleted callback finishes to avoid race condition.
 	// The callback is async but Terminal/ExecaTerminal don't await it, so we track completion
@@ -242,8 +289,10 @@ export async function executeCommandInTerminal(
 
 			// Continue sending compressed output to webview for UI display (unchanged behavior)
 			const compressedOutput = Terminal.compressTerminalOutput(accumulatedOutput)
+			latestCompressedOutput = compressedOutput
 			const status: CommandExecutionStatus = { executionId, status: "output", output: compressedOutput }
 			provider?.postMessageToWebview({ type: "commandExecutionStatus", text: JSON.stringify(status) })
+			schedulePartialCommandOutputUpdate()
 
 			if (runInBackground || hasAskedForCommandOutput) {
 				return
@@ -266,6 +315,9 @@ export async function executeCommandInTerminal(
 		},
 		onCompleted: async (output: string | undefined) => {
 			try {
+				clearTimeout(pendingCommandOutputEmitTimer)
+				pendingCommandOutputEmitTimer = undefined
+
 				// Finalize interceptor and get persisted result.
 				// We await finalize() to ensure the artifact file is fully flushed
 				// before we advertise the artifact_id to the LLM.
@@ -275,8 +327,12 @@ export async function executeCommandInTerminal(
 
 				// Continue using compressed output for UI display
 				result = Terminal.compressTerminalOutput(output ?? "")
+				latestCompressedOutput = result
 
-				task.say("command_output", result)
+				// Preserve order: wait for queued partial updates, then emit the final
+				// non-partial command_output update.
+				await commandOutputSayChain
+				await queueCommandOutputMessage(result, false, true)
 				completed = true
 			} finally {
 				// Signal that onCompleted has finished, so the main code can safely use persistedResult
@@ -372,6 +428,7 @@ export async function executeCommandInTerminal(
 	} finally {
 		clearTimeout(agentTimeoutId)
 		clearTimeout(userTimeoutId)
+		clearTimeout(pendingCommandOutputEmitTimer)
 		task.terminalProcess = undefined
 	}