diff --git a/src/compaction.ts b/src/compaction.ts
index e2a20b2..e93152a 100644
--- a/src/compaction.ts
+++ b/src/compaction.ts
@@ -4,11 +4,14 @@ import type { CompactionSource, ExtensionState } from "./state.js";
 /** Runtime compaction-source detection between input → before_compact → session_compact (SPEC §8). */
 export interface CompactionRuntime {
 	pendingCompactionSource: CompactionSource | null;
+	/** Manual compaction with default settings: clear stale pending on next user prompt (SPEC §16.5, §12.3). */
+	clearPendingReinjectOnNextUserInput: boolean;
 }
 
 export function createCompactionRuntime(): CompactionRuntime {
 	return {
 		pendingCompactionSource: null,
+		clearPendingReinjectOnNextUserInput: false,
 	};
 }
 
@@ -51,8 +54,14 @@ export function consumeCompactionOnSessionCompact(
 	sessionOverride: boolean | null,
 	settings: SkillReinjectSettings,
 ): boolean {
+	const source = runtime.pendingCompactionSource;
 	const shouldReinject = shouldReinjectAfterCompaction(sessionOverride, settings, runtime);
-	state.lastCompactionSource = runtime.pendingCompactionSource;
+	state.lastCompactionSource = source;
+	if (source === "manual" && !settings.reinjectOnManualCompaction) {
+		runtime.clearPendingReinjectOnNextUserInput = true;
+	} else if (source === "auto" && shouldReinject) {
+		runtime.clearPendingReinjectOnNextUserInput = false;
+	}
 	runtime.pendingCompactionSource = null;
 	return shouldReinject;
 }
diff --git a/src/index.ts b/src/index.ts
index cc05330..0d61010 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -16,6 +16,7 @@ import {
 } from "./compaction.js";
 import { detectSlashSkill, matchReadPathToSkillWhenEnabled, parseSkillBlocksFromText, userMessageText } from "./detect.js";
 import {
+	clearPendingReinjectOnUserPrompt,
 	enqueueDeferredReinjectFromCompact,
 	planReinject,
 	sendImmediateReinjectAllFollowUp,
@@ -147,7 +148,13 @@ export default function skillReinject(pi: ExtensionAPI): void {
 
 		const settings = readSettings(ctx);
 		const pendingBefore = state.pendingReinject.length;
-		const deferred = tryConsumeDeferredReinject(state, settings, registeredSkills, ctx);
+		const deferred = tryConsumeDeferredReinject(
+			state,
+			settings,
+			registeredSkills,
+			ctx,
+			compactionRuntime,
+		);
 		if (pendingBefore > 0) {
 			persistState();
 		}
@@ -163,6 +170,10 @@ export default function skillReinject(pi: ExtensionAPI): void {
 
 		markManualCompactionFromInput(event.text, compactionRuntime);
 
+		if (clearPendingReinjectOnUserPrompt(state, compactionRuntime)) {
+			persistState();
+		}
+
 		const skillName = detectSlashSkill(event.text);
 		if (skillName) {
 			const skills = resolveRegisteredSkills(ctx.cwd, registeredSkills);
diff --git a/src/reinject.ts b/src/reinject.ts
index b7adb78..41c3bb3 100644
--- a/src/reinject.ts
+++ b/src/reinject.ts
@@ -13,6 +13,7 @@ import {
 	skillsPresentInKeptWindow,
 } from "./kept.js";
 import type { SkillReinjectSettings } from "./settings.js";
+import type { CompactionRuntime } from "./compaction.js";
 import type { ExtensionState } from "./state.js";
 
 export const DEFERRED_REINJECT_CUSTOM_TYPE = "skill-reinject:inject";
@@ -173,16 +174,37 @@ export function reinjectNow(
 	sendImmediateReinjectAllFollowUp(pi, skillNames, state, settings, registeredSkills, ctx);
 }
 
+/**
+ * Manual `/compact` with default settings: drop stale pending on the next user prompt (SPEC §16.5, §12.3).
+ * Returns true when pending was cleared.
+ */
+export function clearPendingReinjectOnUserPrompt(
+	state: ExtensionState,
+	compactionRuntime: CompactionRuntime,
+): boolean {
+	if (!compactionRuntime.clearPendingReinjectOnNextUserInput) {
+		return false;
+	}
+	compactionRuntime.clearPendingReinjectOnNextUserInput = false;
+	const hadPending = state.pendingReinject.length > 0;
+	state.pendingReinject = [];
+	return hadPending;
+}
+
 /**
  * Defer path on before_agent_start: inject one combined message, then clear queue (SPEC §6.5.1).
- * Returns undefined when pendingReinject is empty.
+ * Returns undefined when pendingReinject is empty or manual compaction scheduled a clear (SPEC §16.5).
  */
 export function tryConsumeDeferredReinject(
 	state: ExtensionState,
 	settings: SkillReinjectSettings,
 	registeredSkills: readonly Pick<Skill, "name" | "filePath" | "baseDir">[],
 	ctx?: ExtensionContext,
+	compactionRuntime?: CompactionRuntime,
 ): BeforeAgentStartEventResult | undefined {
+	if (compactionRuntime?.clearPendingReinjectOnNextUserInput) {
+		return undefined;
+	}
 	if (state.pendingReinject.length === 0) {
 		return undefined;
 	}
diff --git a/test/reinject-manual-defer.test.ts b/test/reinject-manual-defer.test.ts
new file mode 100644
index 0000000..52ddfdf
--- /dev/null
+++ b/test/reinject-manual-defer.test.ts
@@ -0,0 +1,75 @@
+import { describe, expect, it } from "vitest";
+import {
+	consumeCompactionOnSessionCompact,
+	createCompactionRuntime,
+} from "../src/compaction";
+import { clearPendingReinjectOnUserPrompt, tryConsumeDeferredReinject } from "../src/reinject";
+import { createDefaultSettings } from "../src/settings";
+import { createInitialState } from "../src/state";
+
+describe("manual compaction defer clear", () => {
+	it("schedules clear on manual compaction when reinjectOnManualCompaction is false", () => {
+		const runtime = createCompactionRuntime();
+		const state = createInitialState();
+		state.pendingReinject = ["alpha"];
+		runtime.pendingCompactionSource = "manual";
+
+		const shouldReinject = consumeCompactionOnSessionCompact(runtime, state, null, createDefaultSettings());
+
+		expect(shouldReinject).toBe(false);
+		expect(runtime.clearPendingReinjectOnNextUserInput).toBe(true);
+		expect(state.pendingReinject).toEqual(["alpha"]);
+	});
+
+	it("blocks deferred inject until user prompt clears stale pending", () => {
+		const runtime = createCompactionRuntime();
+		const state = createInitialState();
+		state.pendingReinject = ["alpha"];
+		runtime.clearPendingReinjectOnNextUserInput = true;
+
+		expect(
+			tryConsumeDeferredReinject(state, createDefaultSettings(), [], undefined, runtime),
+		).toBeUndefined();
+		expect(state.pendingReinject).toEqual(["alpha"]);
+	});
+
+	it("clears pending on user prompt and allows deferred inject again", () => {
+		const runtime = createCompactionRuntime();
+		const state = createInitialState();
+		state.pendingReinject = ["alpha"];
+		runtime.clearPendingReinjectOnNextUserInput = true;
+
+		expect(clearPendingReinjectOnUserPrompt(state, runtime)).toBe(true);
+		expect(state.pendingReinject).toEqual([]);
+		expect(runtime.clearPendingReinjectOnNextUserInput).toBe(false);
+	});
+
+	it("does not schedule clear when manual compaction may reinject", () => {
+		const runtime = createCompactionRuntime();
+		const state = createInitialState();
+		state.pendingReinject = ["alpha"];
+		runtime.pendingCompactionSource = "manual";
+		const settings = createDefaultSettings();
+		settings.reinjectOnManualCompaction = true;
+
+		const shouldReinject = consumeCompactionOnSessionCompact(runtime, state, true, settings);
+
+		expect(shouldReinject).toBe(true);
+		expect(runtime.clearPendingReinjectOnNextUserInput).toBe(false);
+	});
+
+	it("clears stale manual flag when a later auto compaction enqueues reinject", () => {
+		const runtime = createCompactionRuntime();
+		const state = createInitialState();
+		runtime.clearPendingReinjectOnNextUserInput = true;
+		state.pendingReinject = ["beta"];
+		runtime.pendingCompactionSource = "auto";
+
+		const shouldReinject = consumeCompactionOnSessionCompact(runtime, state, true, createDefaultSettings());
+
+		expect(shouldReinject).toBe(true);
+		expect(runtime.clearPendingReinjectOnNextUserInput).toBe(false);
+		expect(clearPendingReinjectOnUserPrompt(state, runtime)).toBe(false);
+		expect(state.pendingReinject).toEqual(["beta"]);
+	});
+});