diff --git a/src/services/sync/ChromaMcpManager.ts b/src/services/sync/ChromaMcpManager.ts
index 1ac78298..b7108b8c 100644
--- a/src/services/sync/ChromaMcpManager.ts
+++ b/src/services/sync/ChromaMcpManager.ts
@@ -116,10 +116,16 @@ export class ChromaMcpManager {
       args: uvxSpawnArgs.join(' ')
     });
 
+    // Run chroma-mcp from the home directory so that pydantic-settings (used
+    // by chroma-mcp internally) does not pick up .env / .env.local files from
+    // the project directory. Those files often contain project-specific vars
+    // that pydantic rejects with "Extra inputs are not permitted", crashing the
+    // subprocess immediately. Fixes #1297.
     this.transport = new StdioClientTransport({
       command: uvxSpawnCommand,
       args: uvxSpawnArgs,
       env: spawnEnvironment,
+      cwd: os.homedir(),
       stderr: 'pipe'
     });
 
diff --git a/tests/services/sync/chroma-mcp-manager-cwd.test.ts b/tests/services/sync/chroma-mcp-manager-cwd.test.ts
new file mode 100644
index 00000000..508336dd
--- /dev/null
+++ b/tests/services/sync/chroma-mcp-manager-cwd.test.ts
@@ -0,0 +1,53 @@
+import { describe, it, expect, mock } from 'bun:test';
+import os from 'os';
+import { readFileSync } from 'fs';
+import { join } from 'path';
+
+/**
+ * Regression test for issue #1297.
+ *
+ * When the worker spawns chroma-mcp via StdioClientTransport, if the CWD is
+ * the project directory and that directory contains a .env.local file with
+ * non-chroma env vars, pydantic-settings crashes with "Extra inputs are not
+ * permitted". The fix is to set `cwd: os.homedir()` so pydantic never reads
+ * the project's env files.
+ */
+
+const CHROMA_MCP_MANAGER_PATH = join(
+  import.meta.dir, '..', '..', '..', 'src', 'services', 'sync', 'ChromaMcpManager.ts'
+);
+
+describe('ChromaMcpManager: cwd isolation from project .env files (#1297)', () => {
+  it('StdioClientTransport is constructed with cwd set to homedir', () => {
+    // Source-level assertion: verify the fix is present in the source.
+    // ChromaMcpManager uses StdioClientTransport (from @modelcontextprotocol/sdk),
+    // which we cannot easily import in a unit test without spawning a real process.
+    // A source inspection is the appropriate guardrail here.
+    const source = readFileSync(CHROMA_MCP_MANAGER_PATH, 'utf-8');
+
+    // The StdioClientTransport constructor call must include `cwd: os.homedir()`
+    // (or equivalent) so that pydantic-settings in chroma-mcp does not read
+    // .env.local from the project directory.
+    expect(source).toContain('cwd: os.homedir()');
+  });
+
+  it('the cwd property appears inside the StdioClientTransport constructor call', () => {
+    const source = readFileSync(CHROMA_MCP_MANAGER_PATH, 'utf-8');
+
+    // Locate the StdioClientTransport constructor block and verify cwd is in it.
+    const transportBlockMatch = source.match(
+      /new StdioClientTransport\(\s*\{([\s\S]*?)\}\s*\)/
+    );
+    expect(transportBlockMatch).not.toBeNull();
+
+    const constructorBody = transportBlockMatch![1];
+    expect(constructorBody).toContain('cwd');
+    expect(constructorBody).toContain('homedir');
+  });
+
+  it('os module is imported (required for os.homedir())', () => {
+    const source = readFileSync(CHROMA_MCP_MANAGER_PATH, 'utf-8');
+    // os is already imported in the original file — confirm it's still there
+    expect(source).toMatch(/import os from ['"]os['"]/);
+  });
+});