diff --git a/packages/coding-agent/src/core/agent-session.ts b/packages/coding-agent/src/core/agent-session.ts
index e4f53004b..a0dda03e1 100644
--- a/packages/coding-agent/src/core/agent-session.ts
+++ b/packages/coding-agent/src/core/agent-session.ts
@@ -401,6 +401,7 @@ export class AgentSession {
 	private _unsubscribeAgent?: () => void;
 	private _eventListeners: AgentSessionEventListener[] = [];
 	private _isAgentRunActive = false;
+	private _promptPreflightCount = 0;
 	private _agentRunAbortRequested = false;
 	private _idleWaitPromise: Promise<void> | undefined;
 	private _resolveIdleWait: (() => void) | undefined;
@@ -2135,12 +2136,32 @@ export class AgentSession {
 			}
 		}
 
-		if (this._compactionAbortController !== undefined) {
+		if (this._compactionAbortController !== undefined || this._branchSummaryAbortController !== undefined) {
 			throw new Error(
 				"Cannot submit a prompt while compaction is in progress. Wait for compaction to finish and retry.",
 			);
 		}
 
+		// Reserve the context through async input hooks and auth checks so tree navigation cannot
+		// start meanwhile (#9154). _startRun marks the run active synchronously, so there is no gap.
+		this._promptPreflightCount++;
+		let trigger: BeforeAgentStartTrigger | undefined;
+		try {
+			trigger = await this._preparePrompt(text, options);
+		} finally {
+			this._promptPreflightCount--;
+		}
+		if (trigger) await this._startRun(trigger, () => preflightResult?.("started"));
+	}
+
+	/**
+	 * Run input hooks, expand templates, queue while streaming, and validate model and auth.
+	 * Returns the run trigger, or undefined when the prompt was handled or queued.
+	 */
+	private async _preparePrompt(text: string, options?: PromptOptions): Promise<BeforeAgentStartTrigger | undefined> {
+		const expandPromptTemplates = options?.expandPromptTemplates ?? true;
+		const preflightResult = options?.preflightResult;
+
 		// Emit input event for extension interception (before skill/template expansion)
 		const processedInput = await this._runInputHandlers(
 			text,
@@ -2150,7 +2171,7 @@ export class AgentSession {
 		);
 		if (!processedInput) {
 			preflightResult?.("handled");
-			return;
+			return undefined;
 		}
 		const { text: currentText, images: currentImages } = processedInput;
 
@@ -2174,7 +2195,7 @@ export class AgentSession {
 				await this._queueSteer(expandedText, currentImages);
 			}
 			preflightResult?.("queued");
-			return;
+			return undefined;
 		}
 
 		// Validate model
@@ -2197,9 +2218,7 @@ export class AgentSession {
 			throw new Error(formatNoApiKeyFoundMessage(this.model.provider));
 		}
 
-		await this._startRun({ messageType: "user", prompt: expandedText, images: currentImages }, () =>
-			preflightResult?.("started"),
-		);
+		return { messageType: "user", prompt: expandedText, images: currentImages };
 	}
 
 	/**
@@ -4075,7 +4094,7 @@ export class AgentSession {
 		targetId: string,
 		options: { summarize?: boolean; customInstructions?: string; replaceInstructions?: boolean; label?: string } = {},
 	): Promise<{ editorText?: string; cancelled: boolean; aborted?: boolean; summaryEntry?: BranchSummaryEntry }> {
-		if (this.isStreaming) {
+		if (this.isStreaming || this._promptPreflightCount > 0) {
 			throw new Error("Wait for the current response to finish before navigating the session tree.");
 		}
 		if (this.isCompacting) {
@@ -4125,7 +4144,8 @@ export class AgentSession {
 		};
 
 		// Set up abort controller for summarization
-		this._branchSummaryAbortController = new AbortController();
+		const abortController = new AbortController();
+		this._branchSummaryAbortController = abortController;
 
 		try {
 			let extensionSummary: { summary: string; details?: unknown; usage?: Usage } | undefined;
@@ -4136,7 +4156,7 @@ export class AgentSession {
 				const result = (await this._extensionRunner.emit({
 					type: "session_before_tree",
 					preparation,
-					signal: this._branchSummaryAbortController.signal,
+					signal: abortController.signal,
 				})) as SessionBeforeTreeResult | undefined;
 
 				if (result?.cancel) {
@@ -4165,7 +4185,7 @@ export class AgentSession {
 			let summaryDetails: unknown;
 			let summaryUsage: Usage | undefined;
 			if (options.summarize && entriesToSummarize.length > 0 && !extensionSummary) {
-				const signal = this._branchSummaryAbortController.signal;
+				const signal = abortController.signal;
 				const branchSummarySettings = this.settingsManager.getBranchSummarySettings();
 				const result = await generateBranchSummary(entriesToSummarize, {
 					...(await this._getSummarizationRequestAuth(this.model!, signal)),
@@ -4247,7 +4267,8 @@ export class AgentSession {
 			this._refreshFinalizedContext();
 			this._restoreToolsFromTranscript();
 
-			// Emit session_tree event
+			// The selected context is installed; session_tree handlers may now prompt or navigate again.
+			this._branchSummaryAbortController = undefined;
 			await this._extensionRunner.emit({
 				type: "session_tree",
 				newLeafId: this.sessionManager.getLeafId(),
@@ -4260,7 +4281,10 @@ export class AgentSession {
 
 			return { editorText, cancelled: false, summaryEntry };
 		} finally {
-			this._branchSummaryAbortController = undefined;
+			// A navigation started from session_tree owns the controller now; do not clear it.
+			if (this._branchSummaryAbortController === abortController) {
+				this._branchSummaryAbortController = undefined;
+			}
 			this._resolveIdleWaitIfIdle();
 		}
 	}
diff --git a/packages/coding-agent/test/suite/regressions/9154-prompt-during-tree-navigation.test.ts b/packages/coding-agent/test/suite/regressions/9154-prompt-during-tree-navigation.test.ts
new file mode 100644
index 000000000..585ae0edf
--- /dev/null
+++ b/packages/coding-agent/test/suite/regressions/9154-prompt-during-tree-navigation.test.ts
@@ -0,0 +1,273 @@
+import { fauxAssistantMessage } from "@earendil-works/pi-ai";
+import { afterEach, describe, expect, it, vi } from "vitest";
+import { assistantMsg, userMsg } from "../../utilities.ts";
+import { createHarness, getMessageText, getUserTexts, type Harness } from "../harness.ts";
+
+function deferred(): { promise: Promise<void>; resolve: () => void } {
+	let resolve!: () => void;
+	const promise = new Promise<void>((done) => {
+		resolve = done;
+	});
+	return { promise, resolve };
+}
+
+function seedHistory(harness: Harness): string {
+	harness.sessionManager.appendMessage(userMsg("first prompt"));
+	const targetId = harness.sessionManager.appendMessage(assistantMsg("first response"));
+	harness.sessionManager.appendMessage(userMsg("second prompt"));
+	harness.sessionManager.appendMessage(assistantMsg("second response"));
+	harness.session.refreshContext();
+	return targetId;
+}
+
+describe("issue #9154: prompt during tree navigation", () => {
+	const harnesses: Harness[] = [];
+
+	afterEach(() => {
+		while (harnesses.length > 0) {
+			harnesses.pop()?.cleanup();
+		}
+	});
+
+	it("rejects a prompt while branch summarization is in progress", async () => {
+		const summaryStarted = deferred();
+		const summaryReleased = deferred();
+
+		const harness = await createHarness({
+			extensionFactories: [
+				(pi) => {
+					pi.on("session_before_tree", async () => {
+						summaryStarted.resolve();
+						await summaryReleased.promise;
+						return { summary: { summary: "abandoned branch summary" } };
+					});
+				},
+			],
+		});
+		harnesses.push(harness);
+
+		const targetId = seedHistory(harness);
+		harness.setResponses([fauxAssistantMessage("unexpected response")]);
+
+		const navigationPromise = harness.session.navigateTree(targetId, { summarize: true });
+		await summaryStarted.promise;
+
+		const preflightResult = vi.fn();
+		let promptError: unknown;
+		try {
+			await harness.session.prompt("prompt during summary", {
+				source: "rpc",
+				preflightResult,
+			});
+		} catch (error) {
+			promptError = error;
+		} finally {
+			summaryReleased.resolve();
+			await navigationPromise;
+		}
+
+		const persistedUserTexts = harness.sessionManager
+			.getEntries()
+			.flatMap((entry) =>
+				entry.type === "message" && entry.message.role === "user" ? [getMessageText(entry.message)] : [],
+			);
+
+		expect(preflightResult).not.toHaveBeenCalled();
+		expect(promptError).toEqual(
+			expect.objectContaining({ message: expect.stringContaining("compaction is in progress") }),
+		);
+		expect(getUserTexts(harness)).not.toContain("prompt during summary");
+		expect(persistedUserTexts).not.toContain("prompt during summary");
+		expect(harness.eventsOfType("agent_start")).toHaveLength(0);
+		expect(harness.eventsOfType("agent_settled")).toHaveLength(0);
+	});
+
+	// The inverse order also loses the completed prompt when navigation rebuilds the context.
+	it.each(["input", "before_agent_start"] as const)("rejects navigation during an awaited %s hook", async (hook) => {
+		const promptStarted = deferred();
+		const promptReleased = deferred();
+		const treeStarted = deferred();
+		const treeReleased = deferred();
+		const harness = await createHarness({
+			extensionFactories: [
+				(pi) => {
+					const pause = async () => {
+						promptStarted.resolve();
+						await promptReleased.promise;
+					};
+					if (hook === "input") pi.on("input", pause);
+					else pi.on("before_agent_start", pause);
+					pi.on("session_before_tree", async () => {
+						treeStarted.resolve();
+						await treeReleased.promise;
+					});
+				},
+			],
+		});
+		harnesses.push(harness);
+		const targetId = seedHistory(harness);
+		harness.setResponses([fauxAssistantMessage("response to racing prompt")]);
+		const prompt = harness.session.prompt("racing prompt", { source: "rpc" });
+		await promptStarted.promise;
+		const navigation = harness.session.navigateTree(targetId).then(
+			() => undefined,
+			(error: unknown) => error,
+		);
+		await Promise.race([treeStarted.promise, navigation]);
+		try {
+			promptReleased.resolve();
+			await prompt;
+		} finally {
+			promptReleased.resolve();
+			treeReleased.resolve();
+		}
+		const navigationError = await navigation;
+		expect(navigationError).toEqual(
+			expect.objectContaining({
+				message: "Wait for the current response to finish before navigating the session tree.",
+			}),
+		);
+		expect(getUserTexts(harness)).toContain("racing prompt");
+		expect(harness.session.messages.map(getMessageText)).toContain("response to racing prompt");
+		await expect(harness.session.navigateTree(targetId)).resolves.toMatchObject({ cancelled: false });
+	});
+
+	it.each(["handled", "rejected"] as const)(
+		"allows navigation after a prompt is %s during preflight",
+		async (outcome) => {
+			const harness = await createHarness({
+				withConfiguredAuth: outcome !== "rejected",
+				extensionFactories: [
+					(pi) => {
+						if (outcome === "handled") pi.on("input", async () => ({ action: "handled" }));
+					},
+				],
+			});
+			harnesses.push(harness);
+			const targetId = seedHistory(harness);
+			const prompt = harness.session.prompt("not sent to the model");
+			if (outcome === "handled") await prompt;
+			else await expect(prompt).rejects.toThrow("No API key");
+			await expect(harness.session.navigateTree(targetId)).resolves.toMatchObject({ cancelled: false });
+		},
+	);
+
+	it("keeps navigation blocked when another prompt finishes preflight first", async () => {
+		const started = deferred();
+		const released = deferred();
+		const harness = await createHarness({
+			extensionFactories: [
+				(pi) => {
+					pi.on("input", async (event) => {
+						if (event.text === "waiting prompt") {
+							started.resolve();
+							await released.promise;
+						}
+						return { action: "handled" };
+					});
+				},
+			],
+		});
+		harnesses.push(harness);
+		const targetId = seedHistory(harness);
+		const waiting = harness.session.prompt("waiting prompt");
+		await started.promise;
+		try {
+			await harness.session.prompt("handled immediately");
+			await expect(harness.session.navigateTree(targetId)).rejects.toThrow(
+				"Wait for the current response to finish before navigating the session tree.",
+			);
+		} finally {
+			released.resolve();
+			await waiting;
+		}
+		await expect(harness.session.navigateTree(targetId)).resolves.toMatchObject({ cancelled: false });
+	});
+
+	it("allows a prompt from session_tree after the selected context is installed", async () => {
+		const errors: string[] = [];
+		const harness = await createHarness({
+			extensionFactories: [
+				(pi) => {
+					pi.on("session_tree", async () => {
+						await harness.session.sendUserMessage("continue on the selected branch");
+					});
+				},
+			],
+		});
+		harnesses.push(harness);
+		await harness.session.bindExtensions({ onError: (error) => errors.push(error.error) });
+		const targetId = seedHistory(harness);
+		harness.setResponses([fauxAssistantMessage("continued")]);
+		await harness.session.navigateTree(targetId);
+		expect(errors).toEqual([]);
+		expect(getUserTexts(harness)).toEqual(["first prompt", "continue on the selected branch"]);
+		expect(harness.session.getLastAssistantText()).toBe("continued");
+	});
+
+	it("does not clear a new navigation started from session_tree", async () => {
+		const started = deferred();
+		const released = deferred();
+		let nextTargetId = "";
+		let continuation: Promise<unknown> | undefined;
+		const harness = await createHarness({
+			extensionFactories: [
+				(pi) => {
+					pi.on("session_before_tree", async (event) => {
+						if (event.preparation.targetId === nextTargetId) {
+							started.resolve();
+							await released.promise;
+						}
+					});
+					pi.on("session_tree", () => {
+						continuation ??= harness.session.navigateTree(nextTargetId).then(
+							() => undefined,
+							(error: unknown) => error,
+						);
+					});
+				},
+			],
+		});
+		harnesses.push(harness);
+		const targetId = seedHistory(harness);
+		nextTargetId = harness.sessionManager.getLeafId()!;
+		try {
+			await harness.session.navigateTree(targetId);
+			expect(continuation).toBeDefined();
+			await Promise.race([started.promise, continuation]);
+			expect(harness.session.isCompacting).toBe(true);
+			await expect(harness.session.prompt("must wait for the second navigation")).rejects.toThrow(
+				"compaction is in progress",
+			);
+		} finally {
+			released.resolve();
+			await continuation;
+		}
+		expect(await continuation).toBeUndefined();
+		expect(harness.sessionManager.getLeafId()).toBe(nextTargetId);
+		expect(harness.session.isCompacting).toBe(false);
+	});
+
+	it.each(["command", "agent_settled"] as const)("allows navigation from an extension %s", async (event) => {
+		let targetId = "";
+		let navigated = false;
+		const harness = await createHarness({
+			extensionFactories: [
+				(pi) => {
+					const navigate = async () => {
+						await harness.session.navigateTree(targetId);
+						navigated = true;
+					};
+					if (event === "command") pi.registerCommand("rewind", { handler: navigate });
+					else pi.on("agent_settled", navigate);
+				},
+			],
+		});
+		harnesses.push(harness);
+		targetId = seedHistory(harness);
+		harness.setResponses([fauxAssistantMessage("done")]);
+		await harness.session.prompt(event === "command" ? "/rewind" : "finish then rewind");
+		expect(navigated).toBe(true);
+		expect(harness.sessionManager.getLeafId()).toBe(targetId);
+	});
+});