diff --git a/apps/backend/core/worktree.py b/apps/backend/core/worktree.py
index 55a3a79e0e..22f727f4bf 100644
--- a/apps/backend/core/worktree.py
+++ b/apps/backend/core/worktree.py
@@ -39,6 +39,11 @@
 
 T = TypeVar("T")
 
+# Detects an existing `ignore-workspace=...` directive in a .npmrc, regardless
+# of leading whitespace. Used to decide whether to append it when the host repo
+# already commits a .npmrc (registry/auth config) into worktrees.
+_IGNORE_WORKSPACE_PATTERN = re.compile(r"^\s*ignore-workspace\s*=", re.MULTILINE)
+
 
 def _is_retryable_network_error(stderr: str) -> bool:
     """Check if an error is a retryable network/connection issue."""
@@ -733,6 +738,31 @@ def create_worktree(self, spec_name: str) -> WorktreeInfo:
 
         print(f"Created worktree: {worktree_path.name} on branch {branch_name}")
 
+        # Write .npmrc to prevent pnpm/npm from walking up to the parent
+        # workspace root (pnpm-workspace.yaml / package.json#workspaces).
+        # Without this, running `pnpm install` inside the worktree silently
+        # re-links the parent repo's node_modules into the worktree's pnpm
+        # store, corrupting the parent's dependency graph after cleanup.
+        # See: https://pnpm.io/npmrc#ignore-workspace
+        # If the host repo already commits a .npmrc (registry/auth config), we
+        # append the directive instead of skipping — otherwise the workspace
+        # fix gets bypassed silently for monorepos that need it most.
+        npmrc_path = worktree_path / ".npmrc"
+        try:
+            existing = npmrc_path.read_text(encoding="utf-8") if npmrc_path.exists() else ""
+            if not _IGNORE_WORKSPACE_PATTERN.search(existing):
+                separator = "" if not existing or existing.endswith("\n") else "\n"
+                npmrc_path.write_text(
+                    existing + separator + "ignore-workspace=true\n",
+                    encoding="utf-8",
+                )
+                logger.debug(
+                    "Ensured ignore-workspace=true in .npmrc for worktree: %s",
+                    worktree_path,
+                )
+        except OSError as e:
+            logger.warning("Could not write .npmrc to worktree %s: %s", worktree_path, e)
+
         return WorktreeInfo(
             path=worktree_path,
             branch=branch_name,
diff --git a/apps/frontend/src/main/ipc-handlers/terminal/worktree-handlers.ts b/apps/frontend/src/main/ipc-handlers/terminal/worktree-handlers.ts
index b241fba7f6..cfc98af5d0 100644
--- a/apps/frontend/src/main/ipc-handlers/terminal/worktree-handlers.ts
+++ b/apps/frontend/src/main/ipc-handlers/terminal/worktree-handlers.ts
@@ -834,6 +834,27 @@ async function createTerminalWorktree(
       debugLog('[TerminalWorktree] Created worktree in detached HEAD mode from', baseRef);
     }
 
+    // Write .npmrc to prevent pnpm/npm from walking up to the parent
+    // workspace root (pnpm-workspace.yaml / package.json#workspaces).
+    // Without this, running `pnpm install` inside the worktree silently
+    // re-links the parent repo's node_modules into the worktree's pnpm
+    // store, corrupting the parent's dependency graph after cleanup.
+    // See: https://pnpm.io/npmrc#ignore-workspace
+    // If the host repo already commits a .npmrc (registry/auth config), we
+    // append the directive instead of skipping — otherwise the workspace
+    // fix gets bypassed silently for monorepos that need it most.
+    const npmrcPath = path.join(worktreePath, '.npmrc');
+    try {
+      const existing = existsSync(npmrcPath) ? readFileSync(npmrcPath, 'utf-8') : '';
+      if (!/^\s*ignore-workspace\s*=/m.test(existing)) {
+        const separator = !existing || existing.endsWith('\n') ? '' : '\n';
+        writeFileSync(npmrcPath, existing + separator + 'ignore-workspace=true\n', 'utf-8');
+        debugLog('[TerminalWorktree] Ensured ignore-workspace=true in .npmrc for worktree:', worktreePath);
+      }
+    } catch (npmrcError) {
+      debugError('[TerminalWorktree] Could not write .npmrc to worktree:', npmrcError);
+    }
+
     // Set up dependencies (node_modules, venvs, etc.) for tooling support
     // This allows pre-commit hooks to run typecheck without npm install in worktree
     const setupDeps = await setupWorktreeDependencies(projectPath, worktreePath);