diff --git a/.changeset/merge-worktree-canonical-path.md b/.changeset/merge-worktree-canonical-path.md
new file mode 100644
index 0000000000..e4e8f28678
--- /dev/null
+++ b/.changeset/merge-worktree-canonical-path.md
@@ -0,0 +1,3 @@
+"@runfusion/fusion": patch
+
+Fix coding-agent startup from AI merge temp worktrees on macOS by comparing Git worktree paths with filesystem-canonical paths.
diff --git a/packages/engine/src/__tests__/pi-layers-wiring.test.ts b/packages/engine/src/__tests__/pi-layers-wiring.test.ts
index 8c242edbab..c23f354963 100644
--- a/packages/engine/src/__tests__/pi-layers-wiring.test.ts
+++ b/packages/engine/src/__tests__/pi-layers-wiring.test.ts
@@ -26,8 +26,10 @@ const settingsManagerInMemoryMock = vi.fn(() => ({ kind: "settings-manager" }));
 const setFallbackResolverMock = vi.fn();
 const reloadMock = vi.fn(async () => {});
 const execSyncMock = vi.fn((_cmd?: any, _opts?: any) => "");
+const spawnSyncMock = vi.fn(() => ({ status: 1, stdout: "" }));
 const existsSyncMock = vi.fn((_path: PathLike) => false);
 const readFileSyncMock = vi.fn((_path?: any) => "{}");
+const realpathSyncNativeMock = vi.fn((path: PathLike) => String(path));
 const readCustomProvidersMock = vi.fn(() => []);
 
 // Capture DefaultResourceLoader constructor args
@@ -64,7 +66,7 @@ vi.mock("node:child_process", () => {
         }
       });
     });
-  return { execSync: execSyncFn, exec: execFn, execFile: vi.fn() };
+  return { execSync: execSyncFn, exec: execFn, execFile: vi.fn(), spawnSync: spawnSyncMock };
 });
 
 vi.mock("node:fs", async () => {
@@ -73,6 +75,9 @@ vi.mock("node:fs", async () => {
     ...actual,
     existsSync: existsSyncMock,
     readFileSync: readFileSyncMock,
+    realpathSync: Object.assign(vi.fn((path: PathLike) => String(path)), {
+      native: realpathSyncNativeMock,
+    }),
   };
 });
 
@@ -143,8 +148,10 @@ describe("createFnAgent prompt layer wiring", () => {
     vi.clearAllMocks();
     capturedResourceLoaderOptions = null;
     execSyncMock.mockReturnValue("");
+    spawnSyncMock.mockReturnValue({ status: 1, stdout: "" });
     existsSyncMock.mockReturnValue(false);
     readFileSyncMock.mockReturnValue("{}");
+    realpathSyncNativeMock.mockImplementation((path: PathLike) => String(path));
     readCustomProvidersMock.mockReturnValue([]);
     findMock.mockImplementation((provider: string, modelId: string) => ({ provider, id: modelId }));
     createAgentSessionMock.mockResolvedValue({
@@ -174,6 +181,40 @@ describe("createFnAgent prompt layer wiring", () => {
     expect(override).toBe("Stable prefix.");
   });
 
+  it("accepts macOS-canonicalized Git linked worktrees during session validation", async () => {
+    const cwd = "/var/folders/zp/fjh8794n7bl61c_pn1gmdt200000gn/T/project/.worktrees/fn-6085";
+    const projectRoot = "/var/folders/zp/fjh8794n7bl61c_pn1gmdt200000gn/T/project";
+    const canonicalCwd = "/private/var/folders/zp/fjh8794n7bl61c_pn1gmdt200000gn/T/project/.worktrees/fn-6085";
+    existsSyncMock.mockImplementation((path: PathLike) => {
+      const text = String(path);
+      return text === cwd || text === `${cwd}/.git` || text === `${projectRoot}/.fusion`;
+    });
+    realpathSyncNativeMock.mockImplementation((path: PathLike) => {
+      const text = String(path);
+      return text.startsWith("/var/folders/") ? `/private${text}` : text;
+    });
+    execSyncMock.mockImplementation((cmd: string) => {
+      if (cmd.includes("git rev-parse --show-toplevel")) {
+        return `${canonicalCwd}\n`;
+      }
+      if (cmd.includes("git worktree list --porcelain")) {
+        return `worktree ${canonicalCwd}\nHEAD abc123\n`;
+      }
+      return "";
+    });
+
+    const { createFnAgent } = await import("../pi.js");
+
+    await expect(createFnAgent({
+      cwd,
+      systemPrompt: "system",
+      defaultProvider: "mock",
+      defaultModelId: "scripted",
+    })).resolves.toBeDefined();
+
+    expect(createAgentSessionMock).toHaveBeenCalledWith(expect.objectContaining({ cwd }));
+  });
+
   it("passes dynamic layer via appendSystemPromptOverride when layers provided", async () => {
     const { createFnAgent } = await import("../pi.js");
 
diff --git a/packages/engine/src/pi.ts b/packages/engine/src/pi.ts
index 227972480a..3a70ed7e21 100644
--- a/packages/engine/src/pi.ts
+++ b/packages/engine/src/pi.ts
@@ -6,7 +6,7 @@
  */
 
 /* eslint-disable @typescript-eslint/no-explicit-any */
-import { existsSync, readFileSync } from "node:fs";
+import { existsSync, readFileSync, realpathSync } from "node:fs";
 import { exec, execFile } from "node:child_process";
 import { promisify } from "node:util";
 import { createRequire } from "node:module";
@@ -1400,22 +1400,30 @@ async function isRegisteredGitWorktree(projectRoot: string, worktreePath: string
       cwd: projectRoot,
       encoding: "utf-8",
     });
-    const resolvedWorktree = resolve(worktreePath);
+    const resolvedWorktree = normalizeExistingPathForGitComparison(worktreePath);
     return stdout.split("\n").some((line) =>
-      line.startsWith("worktree ") && resolve(line.slice("worktree ".length)) === resolvedWorktree
+      line.startsWith("worktree ") && normalizeExistingPathForGitComparison(line.slice("worktree ".length)) === resolvedWorktree
     );
   } catch {
     return false;
   }
 }
 
+function normalizeExistingPathForGitComparison(path: string): string {
+  try {
+    return realpathSync.native(path);
+  } catch {
+    return resolve(path);
+  }
+}
+
 async function isCompleteGitWorktree(worktreePath: string): Promise<boolean> {
   try {
     const { stdout } = await execAsync("git rev-parse --show-toplevel", {
       cwd: worktreePath,
       encoding: "utf-8",
     });
-    return resolve(stdout.trim()) === resolve(worktreePath);
+    return normalizeExistingPathForGitComparison(stdout.trim()) === normalizeExistingPathForGitComparison(worktreePath);
   } catch {
     return false;
   }