diff --git a/__tests__/domains/config/merger/conflict-resolver.test.ts b/__tests__/domains/config/merger/conflict-resolver.test.ts
index 6d272c6..acb51a3 100644
--- a/__tests__/domains/config/merger/conflict-resolver.test.ts
+++ b/__tests__/domains/config/merger/conflict-resolver.test.ts
@@ -11,8 +11,10 @@ function createMergeResult(): MergeResult {
 		hooksAdded: 0,
 		hooksPreserved: 0,
 		hooksSkipped: 0,
+		hooksRemoved: 0,
 		mcpServersPreserved: 0,
 		mcpServersSkipped: 0,
+		mcpServersRemoved: 0,
 		conflictsDetected: [],
 		newlyInstalledHooks: [],
 		newlyInstalledServers: [],
diff --git a/__tests__/domains/config/merger/merge-engine.test.ts b/__tests__/domains/config/merger/merge-engine.test.ts
new file mode 100644
index 0000000..ba45b4a
--- /dev/null
+++ b/__tests__/domains/config/merger/merge-engine.test.ts
@@ -0,0 +1,150 @@
+import { describe, expect, it } from "bun:test";
+import { mergeHooks, mergeMcp, mergeSettings } from "@/domains/config/merger/merge-engine.js";
+import type { HookEntry, MergeResult, SettingsJson } from "@/domains/config/merger/types.js";
+
+function createMergeResult(): MergeResult {
+	return {
+		merged: {},
+		hooksAdded: 0,
+		hooksPreserved: 0,
+		hooksSkipped: 0,
+		hooksRemoved: 0,
+		mcpServersPreserved: 0,
+		mcpServersSkipped: 0,
+		mcpServersRemoved: 0,
+		conflictsDetected: [],
+		newlyInstalledHooks: [],
+		newlyInstalledServers: [],
+		hooksByOrigin: new Map(),
+	};
+}
+
+describe("merge-engine deprecation removal", () => {
+	describe("mergeHooks removes deprecated hooks", () => {
+		it("should remove hook in installed but not in source", () => {
+			const sourceHooks: Record<string, HookEntry[]> = {
+				SessionStart: [{ type: "command", command: "node new-hook.js" }],
+			};
+			const destHooks: Record<string, HookEntry[]> = {
+				SessionStart: [
+					{ type: "command", command: "node new-hook.js" },
+					{ type: "command", command: "node deprecated-hook.js" },
+				],
+			};
+			const result = createMergeResult();
+
+			const merged = mergeHooks(sourceHooks, destHooks, result, {
+				installedSettings: {
+					hooks: ["node deprecated-hook.js"],
+				},
+			});
+
+			// deprecated-hook.js should be removed
+			expect(merged.SessionStart).toHaveLength(1);
+			expect(result.hooksRemoved).toBe(1);
+			expect(result.removedHooks).toContain("node deprecated-hook.js");
+		});
+
+		it("should preserve user-added hook not in installed", () => {
+			const sourceHooks: Record<string, HookEntry[]> = {
+				SessionStart: [{ type: "command", command: "node ck-hook.js" }],
+			};
+			const destHooks: Record<string, HookEntry[]> = {
+				SessionStart: [
+					{ type: "command", command: "node ck-hook.js" },
+					{ type: "command", command: "node user-hook.js" },
+				],
+			};
+			const result = createMergeResult();
+
+			const merged = mergeHooks(sourceHooks, destHooks, result, {
+				installedSettings: {
+					hooks: ["node ck-hook.js"], // user-hook.js not in installed = user added it
+				},
+			});
+
+			// user-hook.js should be preserved
+			expect(merged.SessionStart).toHaveLength(2);
+			expect(result.hooksRemoved).toBe(0);
+		});
+
+		it("should not remove anything with empty installedSettings", () => {
+			const sourceHooks: Record<string, HookEntry[]> = {
+				SessionStart: [{ type: "command", command: "node new-hook.js" }],
+			};
+			const destHooks: Record<string, HookEntry[]> = {
+				SessionStart: [{ type: "command", command: "node old-hook.js" }],
+			};
+			const result = createMergeResult();
+
+			const merged = mergeHooks(sourceHooks, destHooks, result, {
+				installedSettings: { hooks: [] },
+			});
+
+			// old-hook.js preserved (fresh install scenario)
+			expect(merged.SessionStart).toHaveLength(2);
+			expect(result.hooksRemoved).toBe(0);
+		});
+	});
+
+	describe("mergeMcp removes deprecated servers", () => {
+		it("should remove server in installed but not in source", () => {
+			const sourceMcp: SettingsJson["mcp"] = {
+				servers: { "new-server": { command: "npx new" } },
+			};
+			const destMcp: SettingsJson["mcp"] = {
+				servers: {
+					"new-server": { command: "npx new" },
+					"deprecated-server": { command: "npx old" },
+				},
+			};
+			const result = createMergeResult();
+
+			const merged = mergeMcp(sourceMcp, destMcp, result, {
+				installedSettings: {
+					mcpServers: ["deprecated-server"],
+				},
+			});
+
+			expect(merged?.servers).not.toHaveProperty("deprecated-server");
+			expect(merged?.servers).toHaveProperty("new-server");
+			expect(result.mcpServersRemoved).toBe(1);
+			expect(result.removedMcpServers).toContain("deprecated-server");
+		});
+
+		it("should preserve user-added server not in installed", () => {
+			const sourceMcp: SettingsJson["mcp"] = {
+				servers: { "ck-server": { command: "npx ck" } },
+			};
+			const destMcp: SettingsJson["mcp"] = {
+				servers: {
+					"ck-server": { command: "npx ck" },
+					"user-server": { command: "npx user" },
+				},
+			};
+			const result = createMergeResult();
+
+			const merged = mergeMcp(sourceMcp, destMcp, result, {
+				installedSettings: {
+					mcpServers: ["ck-server"], // user-server not in installed
+				},
+			});
+
+			expect(merged?.servers).toHaveProperty("ck-server");
+			expect(merged?.servers).toHaveProperty("user-server");
+			expect(result.mcpServersRemoved).toBe(0);
+		});
+	});
+
+	describe("mergeSettings initializes removal counters", () => {
+		it("should initialize hooksRemoved and mcpServersRemoved to 0", () => {
+			const source: SettingsJson = {};
+			const dest: SettingsJson = {};
+
+			const result = mergeSettings(source, dest);
+
+			expect(result.hooksRemoved).toBe(0);
+			expect(result.mcpServersRemoved).toBe(0);
+		});
+	});
+});
diff --git a/src/domains/config/merger/merge-engine.ts b/src/domains/config/merger/merge-engine.ts
index a5f61ec..7b3021d 100644
--- a/src/domains/config/merger/merge-engine.ts
+++ b/src/domains/config/merger/merge-engine.ts
@@ -1,14 +1,16 @@
 /**
  * Core merge logic for settings
  */
-import { logger } from "@/shared/logger.js";
+import { logger, normalizeCommand } from "@/shared";
 import { mergeHookEntries } from "./conflict-resolver.js";
+import { extractCommands } from "./diff-calculator.js";
 import type { HookConfig, HookEntry, MergeOptions, MergeResult, SettingsJson } from "./types.js";
 
 /**
  * Merge hooks configurations
  * User hooks are preserved, CK hooks are added (deduplicated by command)
  * Respects user deletions when installedSettings is provided
+ * Removes deprecated hooks (in installed but not in source)
  */
 export function mergeHooks(
 	sourceHooks: Record<string, HookConfig[] | HookEntry[]>,
@@ -20,6 +22,12 @@ export function mergeHooks(
 	const installedHooks = options?.installedSettings?.hooks ?? [];
 	const sourceKit = options?.sourceKit;
 
+	// Extract all commands from source for deprecation check
+	const sourceCommands = new Set<string>();
+	for (const entries of Object.values(sourceHooks)) {
+		extractCommands(entries, sourceCommands);
+	}
+
 	for (const [eventName, sourceEntries] of Object.entries(sourceHooks)) {
 		const destEntries = destHooks[eventName] || [];
 		merged[eventName] = mergeHookEntries(
@@ -32,13 +40,85 @@ export function mergeHooks(
 		);
 	}
 
+	// Remove deprecated hooks: in installedHooks but NOT in source
+	// These are hooks that CK previously installed but no longer ships
+	if (installedHooks.length > 0) {
+		const deprecatedHooks = installedHooks.filter(
+			(hook) => !sourceCommands.has(normalizeCommand(hook)),
+		);
+
+		if (deprecatedHooks.length > 0) {
+			result.removedHooks = result.removedHooks ?? [];
+
+			for (const [eventName, entries] of Object.entries(merged)) {
+				const filtered = removeDeprecatedFromEntries(
+					entries as (HookConfig | HookEntry)[],
+					deprecatedHooks,
+					result,
+				);
+				if (filtered.length > 0) {
+					merged[eventName] = filtered;
+				} else {
+					// Remove empty event arrays
+					delete merged[eventName];
+				}
+			}
+		}
+	}
+
 	return merged;
 }
 
+/**
+ * Remove deprecated hooks from entries array
+ * Returns filtered entries with deprecated hooks removed
+ */
+function removeDeprecatedFromEntries(
+	entries: (HookConfig | HookEntry)[],
+	deprecatedHooks: string[],
+	result: MergeResult,
+): (HookConfig | HookEntry)[] {
+	const deprecatedSet = new Set(deprecatedHooks.map((h) => normalizeCommand(h)));
+	const filtered: (HookConfig | HookEntry)[] = [];
+
+	for (const entry of entries) {
+		if ("hooks" in entry && entry.hooks) {
+			// HookConfig with hooks array - filter individual hooks
+			const remainingHooks = entry.hooks.filter((h) => {
+				if (h.command && deprecatedSet.has(normalizeCommand(h.command))) {
+					result.hooksRemoved++;
+					result.removedHooks?.push(h.command);
+					logger.info(`Removed deprecated hook: ${h.command.slice(0, 60)}...`);
+					return false;
+				}
+				return true;
+			});
+			if (remainingHooks.length > 0) {
+				filtered.push({ ...entry, hooks: remainingHooks });
+			}
+		} else if ("command" in entry) {
+			// Single HookEntry
+			if (deprecatedSet.has(normalizeCommand(entry.command))) {
+				result.hooksRemoved++;
+				result.removedHooks?.push(entry.command);
+				logger.info(`Removed deprecated hook: ${entry.command.slice(0, 60)}...`);
+			} else {
+				filtered.push(entry);
+			}
+		} else {
+			// Unknown structure, keep it
+			filtered.push(entry);
+		}
+	}
+
+	return filtered;
+}
+
 /**
  * Merge MCP configurations
  * User servers are preserved, new CK servers are added
  * Respects user deletions when installedSettings is provided
+ * Removes deprecated servers (in installed but not in source)
  */
 export function mergeMcp(
 	sourceMcp: SettingsJson["mcp"],
@@ -135,6 +215,31 @@ export function mergeMcp(
 		}
 	}
 
+	// Remove deprecated servers: in installedServers but NOT in source
+	// These are servers that CK previously installed but no longer ships
+	if (installedServers.length > 0 && merged.servers) {
+		const sourceServerNames = new Set(Object.keys(sourceMcp.servers || {}));
+		const deprecatedServers = installedServers.filter((server) => !sourceServerNames.has(server));
+
+		if (deprecatedServers.length > 0) {
+			result.removedMcpServers = result.removedMcpServers ?? [];
+
+			for (const serverName of deprecatedServers) {
+				if (serverName in merged.servers) {
+					delete merged.servers[serverName];
+					result.mcpServersRemoved++;
+					result.removedMcpServers.push(serverName);
+					logger.info(`Removed deprecated MCP server: ${serverName}`);
+				}
+			}
+
+			// Clean up empty servers object
+			if (merged.servers && Object.keys(merged.servers).length === 0) {
+				merged.servers = undefined;
+			}
+		}
+	}
+
 	// Copy other MCP keys that don't exist
 	for (const key of Object.keys(sourceMcp)) {
 		if (key !== "servers" && !(key in merged)) {
@@ -163,8 +268,10 @@ export function mergeSettings(
 		hooksAdded: 0,
 		hooksPreserved: 0,
 		hooksSkipped: 0,
+		hooksRemoved: 0,
 		mcpServersPreserved: 0,
 		mcpServersSkipped: 0,
+		mcpServersRemoved: 0,
 		conflictsDetected: [],
 		newlyInstalledHooks: [],
 		newlyInstalledServers: [],
diff --git a/src/domains/config/merger/types.ts b/src/domains/config/merger/types.ts
index ee00003..f8e48cd 100644
--- a/src/domains/config/merger/types.ts
+++ b/src/domains/config/merger/types.ts
@@ -58,8 +58,10 @@ export interface MergeResult {
 	hooksAdded: number;
 	hooksPreserved: number;
 	hooksSkipped: number; // Hooks skipped because user removed them
+	hooksRemoved: number; // Hooks removed because kit no longer ships them
 	mcpServersPreserved: number;
 	mcpServersSkipped: number; // Servers skipped because user removed them
+	mcpServersRemoved: number; // Servers removed because kit no longer ships them
 	mcpServersOverwritten?: number; // Servers overwritten due to timestamp comparison
 	conflictsDetected: string[];
 	// Track what was actually installed (for persistence)
@@ -70,6 +72,9 @@ export interface MergeResult {
 	/** Conflict resolution tracking for summary display */
 	hookConflicts?: HookConflictInfo[];
 	mcpConflicts?: McpConflictInfo[];
+	/** Deprecated entries removed during this merge */
+	removedHooks?: string[];
+	removedMcpServers?: string[];
 }
 
 // Options for merge operations