diff --git a/scripts/provision-worktree.sh b/scripts/provision-worktree.sh
index 7b84acaf..1dd481b1 100644
--- a/scripts/provision-worktree.sh
+++ b/scripts/provision-worktree.sh
@@ -346,7 +346,6 @@ list_base_node_modules_paths() {
       ! -path './.paperclip/*' \
       | sed 's#^\./##'
 }
-
 if [[ -f "$worktree_cwd/package.json" && -f "$worktree_cwd/pnpm-lock.yaml" ]]; then
   needs_install=0
 
diff --git a/server/src/__tests__/workspace-runtime.test.ts b/server/src/__tests__/workspace-runtime.test.ts
index b5e1dc31..3b1bee0d 100644
--- a/server/src/__tests__/workspace-runtime.test.ts
+++ b/server/src/__tests__/workspace-runtime.test.ts
@@ -899,6 +899,106 @@ describe("realizeExecutionWorkspace", () => {
     );
   }, 30_000);
 
+  it("provisions worktree-local pnpm node_modules instead of reusing base-repo links", async () => {
+    const repoRoot = await createTempRepo();
+    await fs.mkdir(path.join(repoRoot, "scripts"), { recursive: true });
+    await fs.mkdir(path.join(repoRoot, "packages", "shared"), { recursive: true });
+    await fs.mkdir(path.join(repoRoot, "server"), { recursive: true });
+    await fs.writeFile(
+      path.join(repoRoot, "package.json"),
+      JSON.stringify(
+        {
+          name: "workspace-root",
+          private: true,
+          packageManager: "pnpm@9.15.4",
+        },
+        null,
+        2,
+      ),
+      "utf8",
+    );
+    await fs.writeFile(
+      path.join(repoRoot, "pnpm-workspace.yaml"),
+      ["packages:", "  - packages/*", "  - server", ""].join("\n"),
+      "utf8",
+    );
+    await fs.writeFile(
+      path.join(repoRoot, "packages", "shared", "package.json"),
+      JSON.stringify(
+        {
+          name: "@repo/shared",
+          version: "1.0.0",
+          private: true,
+          type: "module",
+          exports: "./index.js",
+        },
+        null,
+        2,
+      ),
+      "utf8",
+    );
+    await fs.writeFile(path.join(repoRoot, "packages", "shared", "index.js"), "export const value = 'shared';\n", "utf8");
+    await fs.writeFile(
+      path.join(repoRoot, "server", "package.json"),
+      JSON.stringify(
+        {
+          name: "server",
+          private: true,
+          type: "module",
+          dependencies: {
+            "@repo/shared": "workspace:*",
+          },
+        },
+        null,
+        2,
+      ),
+      "utf8",
+    );
+    await fs.writeFile(path.join(repoRoot, "server", "index.js"), "export {};\n", "utf8");
+    await fs.copyFile(provisionWorktreeScriptPath, path.join(repoRoot, "scripts", "provision-worktree.sh"));
+    await fs.chmod(path.join(repoRoot, "scripts", "provision-worktree.sh"), 0o755);
+    await runPnpm(repoRoot, ["install"]);
+    await runGit(repoRoot, ["add", "."]);
+    await runGit(repoRoot, ["commit", "-m", "Add pnpm workspace fixture"]);
+
+    const workspace = await realizeExecutionWorkspace({
+      base: {
+        baseCwd: repoRoot,
+        source: "project_primary",
+        projectId: "project-1",
+        workspaceId: "workspace-1",
+        repoUrl: null,
+        repoRef: "HEAD",
+      },
+      config: {
+        workspaceStrategy: {
+          type: "git_worktree",
+          branchTemplate: "{{issue.identifier}}-{{slug}}",
+          provisionCommand: "bash ./scripts/provision-worktree.sh",
+        },
+      },
+      issue: {
+        id: "issue-1",
+        identifier: "PAP-551",
+        title: "Provision local workspace dependencies",
+      },
+      agent: {
+        id: "agent-1",
+        name: "Codex Coder",
+        companyId: "company-1",
+      },
+    });
+
+    expect((await fs.lstat(path.join(workspace.cwd, "node_modules"))).isSymbolicLink()).toBe(false);
+    expect((await fs.lstat(path.join(workspace.cwd, "server", "node_modules"))).isSymbolicLink()).toBe(false);
+    await expect(fs.realpath(path.join(workspace.cwd, "server", "node_modules", "@repo", "shared"))).resolves.toBe(
+      await fs.realpath(path.join(workspace.cwd, "packages", "shared")),
+    );
+    await expect(fs.realpath(path.join(repoRoot, "server", "node_modules", "@repo", "shared"))).resolves.toBe(
+      await fs.realpath(path.join(repoRoot, "packages", "shared")),
+    );
+  });
+
   it("records worktree setup and provision operations when a recorder is provided", async () => {
     const repoRoot = await createTempRepo();
     const { recorder, operations } = createWorkspaceOperationRecorderDouble();