diff --git a/src/bun.zig b/src/bun.zig
index 2c2b890429..ee8faf872f 100644
--- a/src/bun.zig
+++ b/src/bun.zig
@@ -286,7 +286,9 @@ pub const OSPathSlice = paths.OSPathSlice;
 pub const OSPathBuffer = paths.OSPathBuffer;
 pub const Path = paths.Path;
 pub const AbsPath = paths.AbsPath;
+pub const AutoAbsPath = paths.AutoAbsPath;
 pub const RelPath = paths.RelPath;
+pub const AutoRelPath = paths.AutoRelPath;
 pub const EnvPath = paths.EnvPath;
 pub const path_buffer_pool = paths.path_buffer_pool;
 pub const w_path_buffer_pool = paths.w_path_buffer_pool;
diff --git a/src/install/pnpm.zig b/src/install/pnpm.zig
index 024463e137..eb7e759639 100644
--- a/src/install/pnpm.zig
+++ b/src/install/pnpm.zig
@@ -242,7 +242,7 @@ pub fn migratePnpmLockfile(
                 continue;
             }
 
-            var pkg_json_path: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+            var pkg_json_path: bun.AutoAbsPath = .initTopLevelDir();
             defer pkg_json_path.deinit();
 
             pkg_json_path.append(importer_path);
@@ -285,7 +285,7 @@ pub fn migratePnpmLockfile(
         var importer_dep_res_versions: bun.StringArrayHashMap(bun.StringArrayHashMap([]const u8)) = .init(allocator);
 
         {
-            var pkg_json_path: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+            var pkg_json_path: bun.AutoAbsPath = .initTopLevelDir();
             defer pkg_json_path.deinit();
 
             pkg_json_path.append("package.json");
@@ -329,6 +329,8 @@ pub fn migratePnpmLockfile(
 
         var pkg_map: bun.StringArrayHashMap(PackageID) = .init(allocator);
 
+        try pkg_map.putNoClobber(bun.fs.FileSystem.instance.top_level_dir, 0);
+
         const workspace_pkgs_off = lockfile.packages.len;
 
         workspaces: for (lockfile.workspace_paths.values()) |workspace_path| {
@@ -348,7 +350,7 @@ pub fn migratePnpmLockfile(
                     .value = .{ .workspace = try string_buf.append(path) },
                 };
 
-                var path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                var path_buf: bun.AutoAbsPath = .initTopLevelDir();
                 defer path_buf.deinit();
 
                 path_buf.append(path);
@@ -445,13 +447,13 @@ pub fn migratePnpmLockfile(
                         if (strings.withoutPrefixIfPossibleComptime(version_without_suffix, "link:")) |link_path| {
                             // create a link package for the workspace dependency only if it doesn't already exist
                             if (dep.version.tag == .workspace) {
-                                var link_path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                                var link_path_buf: bun.AutoAbsPath = .initTopLevelDir();
                                 defer link_path_buf.deinit();
                                 link_path_buf.append(workspace_path);
                                 link_path_buf.join(&.{link_path});
 
                                 for (lockfile.workspace_paths.values()) |existing_workspace_path| {
-                                    var workspace_path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                                    var workspace_path_buf: bun.AutoAbsPath = .initTopLevelDir();
                                     defer workspace_path_buf.deinit();
                                     workspace_path_buf.append(existing_workspace_path.slice(string_buf.bytes.items));
 
@@ -469,7 +471,7 @@ pub fn migratePnpmLockfile(
                                 .resolution = .init(.{ .symlink = try string_buf.append(link_path) }),
                             };
 
-                            var abs_link_path: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                            var abs_link_path: bun.AutoAbsPath = .initTopLevelDir();
                             defer abs_link_path.deinit();
 
                             abs_link_path.join(&.{ workspace_path, link_path });
@@ -685,7 +687,7 @@ pub fn migratePnpmLockfile(
             // implicit workspace dependencies
             if (dep.behavior.isWorkspace()) {
                 const workspace_path = dep.version.value.workspace.slice(string_buf);
-                var path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                var path_buf: bun.AutoAbsPath = .initTopLevelDir();
                 defer path_buf.deinit();
                 path_buf.join(&.{workspace_path});
                 if (pkg_map.get(path_buf.slice())) |workspace_pkg_id| {
@@ -706,7 +708,7 @@ pub fn migratePnpmLockfile(
             const version_without_suffix = removeSuffix(version);
 
             if (strings.withoutPrefixIfPossibleComptime(version_without_suffix, "link:")) |maybe_symlink_or_folder_or_workspace_path| {
-                var path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                var path_buf: bun.AutoAbsPath = .initTopLevelDir();
                 defer path_buf.deinit();
                 path_buf.join(&.{maybe_symlink_or_folder_or_workspace_path});
                 if (pkg_map.get(path_buf.slice())) |pkg_id| {
@@ -755,7 +757,7 @@ pub fn migratePnpmLockfile(
             const version_without_suffix = removeSuffix(version);
 
             if (strings.withoutPrefixIfPossibleComptime(version_without_suffix, "link:")) |maybe_symlink_or_folder_or_workspace_path| {
-                var path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                var path_buf: bun.AutoAbsPath = .initTopLevelDir();
                 defer path_buf.deinit();
                 path_buf.join(&.{ workspace_path, maybe_symlink_or_folder_or_workspace_path });
                 if (pkg_map.get(path_buf.slice())) |link_pkg_id| {
@@ -795,8 +797,11 @@ pub fn migratePnpmLockfile(
             switch (dep.version.tag) {
                 .folder, .symlink, .workspace => {
                     const maybe_symlink_or_folder_or_workspace_path = strings.withoutPrefixComptime(version_without_suffix, "link:");
-                    if (pkg_map.get(maybe_symlink_or_folder_or_workspace_path)) |workspace_pkg_id| {
-                        lockfile.buffers.resolutions.items[dep_id] = workspace_pkg_id;
+                    var path_buf: bun.AutoAbsPath = .initTopLevelDir();
+                    defer path_buf.deinit();
+                    path_buf.join(&.{maybe_symlink_or_folder_or_workspace_path});
+                    if (pkg_map.get(path_buf.slice())) |link_pkg_id| {
+                        lockfile.buffers.resolutions.items[dep_id] = link_pkg_id;
                         continue;
                     }
                 },
@@ -1172,7 +1177,7 @@ fn parseAppendImporterDependencies(
                     continue;
                 }
 
-                var path_buf: bun.AbsPath(.{ .sep = .auto }) = .initTopLevelDir();
+                var path_buf: bun.AutoAbsPath = .initTopLevelDir();
                 defer path_buf.deinit();
 
                 path_buf.append(path);
diff --git a/src/paths.zig b/src/paths.zig
index 449d3d9154..74aa7ddea2 100644
--- a/src/paths.zig
+++ b/src/paths.zig
@@ -1,6 +1,8 @@
 pub const Path = paths.Path;
 pub const AbsPath = paths.AbsPath;
+pub const AutoAbsPath = paths.AutoAbsPath;
 pub const RelPath = paths.RelPath;
+pub const AutoRelPath = paths.AutoRelPath;
 
 pub const EnvPath = @import("./paths/EnvPath.zig").EnvPath;
 
diff --git a/src/paths/Path.zig b/src/paths/Path.zig
index 2eb2e06caf..363f69f180 100644
--- a/src/paths/Path.zig
+++ b/src/paths/Path.zig
@@ -227,12 +227,16 @@ pub fn AbsPath(comptime opts: Options) type {
     return Path(copy);
 }
 
+pub const AutoAbsPath = Path(.{ .kind = .abs, .sep = .auto });
+
 pub fn RelPath(comptime opts: Options) type {
     var copy = opts;
     copy.kind = .rel;
     return Path(copy);
 }
 
+pub const AutoRelPath = Path(.{ .kind = .rel, .sep = .auto });
+
 pub fn Path(comptime opts: Options) type {
     const Result = opts.ResultFn();
 
diff --git a/test/cli/install/migration/pnpm-migration.test.ts b/test/cli/install/migration/pnpm-migration.test.ts
index 6bf6e4d91e..5ce3d4219e 100644
--- a/test/cli/install/migration/pnpm-migration.test.ts
+++ b/test/cli/install/migration/pnpm-migration.test.ts
@@ -83,17 +83,53 @@ describe.todo("patched packages", () => {
   });
 });
 
-describe.todo("folder dependencies", () => {
-  test("basic", async () => {
+describe("folder dependencies", () => {
+  test.todo("basic", async () => {
     const { packageDir, packageJson } = await verdaccio.createTestDir({
       files: join(import.meta.dir, "pnpm/folder-dependencies-basic"),
     });
   });
-  test("links are resolved correctly", async () => {
-    // link:
+  test("links to the root package are resolved correctly", async () => {
     const { packageDir, packageJson } = await verdaccio.createTestDir({
-      files: join(import.meta.dir, "pnpm/folder-dependencies-links"),
+      files: join(import.meta.dir, "pnpm/root-package-link-resolution"),
     });
+
+    let proc = spawn({
+      cmd: [bunExe(), "install"],
+      cwd: packageDir,
+      env,
+      stdout: "pipe",
+      stderr: "pipe",
+    });
+
+    const [out, err, exitCode] = await Promise.all([proc.stdout.text(), proc.stderr.text(), proc.exited]);
+
+    expect(exitCode).toBe(0);
+    expect(err).toContain("Saved lockfile");
+
+    expect(
+      await Promise.all([
+        file(join(packageDir, "node_modules", "two-range-deps", "package.json")).json(),
+        file(join(packageDir, "node_modules", "no-deps", "package.json")).json(),
+      ]),
+    ).toMatchInlineSnapshot(`
+      [
+        {
+          "dependencies": {
+            "@types/is-number": ">=1.0.0",
+            "no-deps": "^1.0.0",
+          },
+          "name": "two-range-deps",
+          "version": "1.0.0",
+        },
+        {
+          "dependencies": {
+            "two-range-deps": "1.0.0",
+          },
+          "name": "transitive-root-link-pkg",
+        },
+      ]
+    `);
   });
 });
 
diff --git a/test/cli/install/migration/pnpm/root-package-link-resolution/package.json b/test/cli/install/migration/pnpm/root-package-link-resolution/package.json
new file mode 100644
index 0000000000..6e864da983
--- /dev/null
+++ b/test/cli/install/migration/pnpm/root-package-link-resolution/package.json
@@ -0,0 +1,6 @@
+{
+  "name": "transitive-root-link-pkg",
+  "dependencies": {
+    "two-range-deps": "1.0.0"
+  }
+}
diff --git a/test/cli/install/migration/pnpm/root-package-link-resolution/pnpm-lock.yaml b/test/cli/install/migration/pnpm/root-package-link-resolution/pnpm-lock.yaml
new file mode 100644
index 0000000000..902ae65a92
--- /dev/null
+++ b/test/cli/install/migration/pnpm/root-package-link-resolution/pnpm-lock.yaml
@@ -0,0 +1,35 @@
+lockfileVersion: '9.0'
+
+settings:
+  autoInstallPeers: true
+  excludeLinksFromLockfile: false
+
+importers:
+
+  .:
+    dependencies:
+      two-range-deps:
+        specifier: 1.0.0
+        version: 1.0.0
+
+packages:
+
+  '@types/is-number@2.0.0':
+    resolution: {integrity: sha512-GEeIxCB+NpM1NrDBqmkYPeU8bI//i+xPzdOY4E1YHet51IcFmz4js6k57m69fLl/cbn7sOR7wj9RNNw53X8AiA==}
+
+  no-deps@1.1.0:
+    resolution: {integrity: sha512-ebG2pipYAKINcNI3YxdsiAgFvNGp2gdRwxAKN2LYBm9+YxuH/lHH2sl+GKQTuGiNfCfNZRMHUyyLPEJD6HWm7w==}
+
+  two-range-deps@1.0.0:
+    resolution: {integrity: sha512-N+6kPy/GxuMncNz/EKuIrwdoYbh1qmvHDnw1UbM3sQE184kBn+6qAQgtf1wgT9dJnt6X+tWcTzSmfDvtJikVBA==}
+
+snapshots:
+
+  '@types/is-number@2.0.0': {}
+
+  no-deps@1.1.0: {}
+
+  two-range-deps@1.0.0:
+    dependencies:
+      '@types/is-number': 2.0.0
+      no-deps: 'link:'