diff --git a/toolchains/workspace-pnpm/macros.bzl b/toolchains/workspace-pnpm/macros.bzl
index a333c0725a..34b46d9bb1 100644
--- a/toolchains/workspace-pnpm/macros.bzl
+++ b/toolchains/workspace-pnpm/macros.bzl
@@ -574,17 +574,15 @@ def _npm_test_impl(
 
     pnpm_toolchain = ctx.attrs._workspace_pnpm_toolchain[WorkspacePnpmToolchainInfo]
 
-    exec_cmd = cmd_args(program_run_info, format = "{}::abspath")
-
     run_cmd_args = cmd_args([
         ctx.attrs._python_toolchain[PythonToolchainInfo].interpreter,
         pnpm_toolchain.run_in_dir[DefaultInfo].default_outputs,
         "--cwd",
         cmd_args([build_context.workspace_root, ctx.label.package], delimiter = "/"),
-        "--",
-        exec_cmd,
+        "--bin",
+        cmd_args(program_run_info),
+        program_args,
     ])
-    run_cmd_args.add(program_args)
 
     args_file = ctx.actions.write("args.txt", run_cmd_args)
 
diff --git a/toolchains/workspace-pnpm/run_in_dir.py b/toolchains/workspace-pnpm/run_in_dir.py
index 4c6ce60ee9..2dbb146e70 100644
--- a/toolchains/workspace-pnpm/run_in_dir.py
+++ b/toolchains/workspace-pnpm/run_in_dir.py
@@ -20,6 +20,10 @@ def compute_path(arg: str) -> str:
         "--cwd",
         help="Directory under which to run the program",
     )
+    parser.add_argument(
+        "--bin",
+        help="Binary to execute program with",
+    )
     parser.add_argument(
         "args",
         help="Program and arguments",
@@ -27,17 +31,8 @@ def compute_path(arg: str) -> str:
     )
 
     args = parser.parse_args()
-    args.args.pop(0) # pops the '--' separator off
-
-    cwd = args.cwd
-
-    cmd = []
-    for arg in args.args:
-        cmd.append(compute_path(arg))
+    cmd = [os.path.abspath(args.bin), *args.args]
 
-    exit_code = subprocess.call(cmd, cwd=cwd)
+    exit_code = subprocess.call(cmd, cwd=args.cwd)
 
     sys.exit(exit_code)
-
-
-