diff --git a/packages/server/src/server/workspace-registry-bootstrap-legacy.ts b/packages/server/src/server/workspace-registry-bootstrap-legacy.ts
index e1cea95ad..252a0b313 100644
--- a/packages/server/src/server/workspace-registry-bootstrap-legacy.ts
+++ b/packages/server/src/server/workspace-registry-bootstrap-legacy.ts
@@ -1,8 +1,9 @@
-import { basename, isAbsolute, relative, resolve, sep } from "node:path";
+import { basename, resolve } from "node:path";
 
 import type { ProjectCheckoutLitePayload } from "@getpaseo/protocol/messages";
 
 import { parseGitRevParsePath } from "../utils/git-rev-parse-path.js";
+import { getRealpathAwareRelativePath } from "../utils/path.js";
 import { deriveProjectGroupKey } from "./project-group-key.js";
 import {
   deriveProjectKind,
@@ -80,15 +81,8 @@ function deriveProjectRootPath(input: {
     ? parseGitRevParsePath(input.checkout.worktreeRoot)
     : null;
   if (!worktreeRoot) return input.checkout.mainRepoRoot;
-  const selectedPath = relative(resolve(worktreeRoot), resolve(input.cwd));
-  if (
-    !selectedPath ||
-    selectedPath === "." ||
-    selectedPath === ".." ||
-    selectedPath.startsWith(`..${sep}`) ||
-    isAbsolute(selectedPath)
-  ) {
-    return input.checkout.mainRepoRoot;
-  }
-  return resolve(input.checkout.mainRepoRoot, selectedPath);
+  const selectedPath = getRealpathAwareRelativePath(worktreeRoot, input.cwd);
+  return selectedPath
+    ? resolve(input.checkout.mainRepoRoot, selectedPath)
+    : input.checkout.mainRepoRoot;
 }
diff --git a/packages/server/src/server/workspace-registry-bootstrap.test.ts b/packages/server/src/server/workspace-registry-bootstrap.test.ts
index f4c3a1ca1..f0d37249f 100644
--- a/packages/server/src/server/workspace-registry-bootstrap.test.ts
+++ b/packages/server/src/server/workspace-registry-bootstrap.test.ts
@@ -1,6 +1,6 @@
 import os from "node:os";
 import path from "node:path";
-import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { mkdirSync, mkdtempSync, rmSync, symlinkSync, writeFileSync } from "node:fs";
 
 import { afterEach, beforeEach, describe, expect, test } from "vitest";
 
@@ -456,6 +456,61 @@ describe("bootstrapWorkspaceRegistries", () => {
     );
   });
 
+  test.skipIf(process.platform === "win32")(
+    "maps a symlinked legacy subproject onto the main checkout",
+    async () => {
+      const physicalProject = path.join(GIT_WORKTREE, "packages", "app");
+      const linkedProject = path.join(tmpDir, "app-link");
+      mkdirSync(physicalProject, { recursive: true });
+      symlinkSync(physicalProject, linkedProject, "dir");
+      workspaceGitService = createNoopWorkspaceGitService({
+        getCheckout: async (cwd) => ({
+          cwd,
+          isGit: true,
+          currentBranch: "main",
+          remoteUrl: "git@github.com:acme/legacy-project.git",
+          worktreeRoot: GIT_WORKTREE,
+          isPaseoOwnedWorktree: false,
+          mainRepoRoot: GIT_PROJECT,
+        }),
+      });
+      await agentStorage.initialize();
+      await agentStorage.upsert({
+        id: "linked-app-agent",
+        provider: "codex",
+        cwd: linkedProject,
+        createdAt: "2026-03-01T00:00:00.000Z",
+        updatedAt: "2026-03-02T00:00:00.000Z",
+        lastActivityAt: "2026-03-02T00:00:00.000Z",
+        lastUserMessageAt: null,
+        title: null,
+        labels: {},
+        lastStatus: "idle",
+        lastModeId: null,
+        config: null,
+        runtimeInfo: { provider: "codex", sessionId: null },
+        persistence: null,
+        archivedAt: null,
+      });
+
+      await bootstrapWorkspaceRegistries({
+        paseoHome,
+        agentStorage,
+        projectRegistry,
+        workspaceRegistry,
+        workspaceGitService,
+        logger,
+      });
+
+      expect(await projectRegistry.list()).toEqual([
+        expect.objectContaining({
+          projectId: "remote:github.com/acme/legacy-project#subdir:packages/app",
+          rootPath: path.join(GIT_PROJECT, "packages", "app"),
+        }),
+      ]);
+    },
+  );
+
   test("migrates cwd-only agents to the oldest existing same-cwd workspace", async () => {
     await projectRegistry.initialize();
     await workspaceRegistry.initialize();