diff --git a/examples/genrule/BUILD.bazel b/examples/genrule/BUILD.bazel
index dd176bb965..24b922a956 100644
--- a/examples/genrule/BUILD.bazel
+++ b/examples/genrule/BUILD.bazel
@@ -31,13 +31,12 @@ genrule(
     name = "call_acorn",
     srcs = [
         ":one.js",
-        # reference the location where the "acorn" npm package was linked in our root Bazel package.
-        "//:node_modules/acorn",
         "//:node_modules/acorn/dir",
     ],
     outs = ["out1"],
     cmd = " ".join([
         "$(NODE_PATH)",
+        # reference the location where the "acorn" npm package was linked in the rules_js npm package store.
         "./$(execpath //:node_modules/acorn/dir)/bin/acorn",
         "--compact",
         "$(execpath :one.js)",
@@ -69,7 +68,6 @@ genrule(
         ":require_acorn_js",
         # reference the location where the "acorn" npm package was linked in our root Bazel package.
         "//:node_modules/acorn",
-        "//:node_modules/acorn/dir",
     ],
     outs = ["out2"],
     cmd = """
diff --git a/npm/private/npm_link_package_store.bzl b/npm/private/npm_link_package_store.bzl
index f523bca704..2af66d9b00 100644
--- a/npm/private/npm_link_package_store.bzl
+++ b/npm/private/npm_link_package_store.bzl
@@ -92,7 +92,7 @@ def _npm_link_package_store_impl(ctx):
         )
         files.append(bin_file)
 
-    files_depset = depset(files)
+    files_depset = depset(files, transitive = [store_info.files])
 
     transitive_files_depset = depset(files, transitive = [store_info.transitive_files])
 
diff --git a/npm/private/test/npm_package/BUILD.bazel b/npm/private/test/npm_package/BUILD.bazel
index c671cc78a2..a50110805f 100644
--- a/npm/private/test/npm_package/BUILD.bazel
+++ b/npm/private/test/npm_package/BUILD.bazel
@@ -22,7 +22,19 @@ js_library(
 
 npm_package(
     name = "pkg",
-    srcs = [":lib_a"],
+    srcs = [
+        ":lib_a",
+    ],
+    visibility = ["//visibility:public"],
+)
+
+npm_package(
+    name = "pkg_2",
+    srcs = [
+        ":lib_a",
+        ":node_modules/chalk",  # should be excluded
+        "//:node_modules/chalk",  # should be excluded
+    ],
     visibility = ["//visibility:public"],
 )
 
@@ -40,6 +52,12 @@ diff_test(
     file2 = ":expected_pkg",
 )
 
+diff_test(
+    name = "test_pkg_2",
+    file1 = ":pkg_2",
+    file2 = ":expected_pkg",
+)
+
 npm_package(
     name = "pkg_with_node_modules",
     srcs = [":lib_a"],