diff --git a/packages/node-resolve/src/index.js b/packages/node-resolve/src/index.js
index 9a73b5cfb..0da8f54f2 100644
--- a/packages/node-resolve/src/index.js
+++ b/packages/node-resolve/src/index.js
@@ -57,6 +57,12 @@ export function nodeResolve(opts = {}) {
   let { dedupe } = options;
   let rollupOptions;
 
+  if (moduleDirectories.some((name) => name.includes('/'))) {
+    throw new Error(
+      '`moduleDirectories` option must only contain directory names. If you want to load modules from somewhere not supported by the default module resolution algorithm, see `modulePaths`.'
+    );
+  }
+
   if (typeof dedupe !== 'function') {
     dedupe = (importee) =>
       options.dedupe.includes(importee) || options.dedupe.includes(getPackageName(importee));
diff --git a/packages/node-resolve/test/test.js b/packages/node-resolve/test/test.js
index 15bec442d..a9faff3c7 100755
--- a/packages/node-resolve/test/test.js
+++ b/packages/node-resolve/test/test.js
@@ -273,20 +273,16 @@ test('allows custom moduleDirectories with legacy customResolveOptions.moduleDir
   t.snapshot(warnings);
 });
 
-test('custom moduleDirectories do not support nested dependencies', async (t) => {
-  const warnings = [];
-  const bundle = await rollup({
-    input: 'custom-module-path/main.js',
-    onwarn: (warning) => warnings.push(warning),
-    plugins: [
+test('moduleDirectories option rejects paths that contain a slash', async (t) => {
+  t.throws(
+    () =>
       nodeResolve({
-        moduleDirectories: [join(process.cwd(), 'custom-module-path/node_modules')]
-      })
-    ]
-  });
-
-  t.is(warnings.length, 1);
-  t.is(bundle.cache.modules.length, 2);
+        moduleDirectories: ['some/path']
+      }),
+    {
+      message: /must only contain directory names/
+    }
+  );
 });
 
 test('allows custom modulePaths', async (t) => {