diff --git a/pyccc/files/directory.py b/pyccc/files/directory.py
index ddadaaf..5d0eb08 100644
--- a/pyccc/files/directory.py
+++ b/pyccc/files/directory.py
@@ -79,11 +79,13 @@ def put(self, destination):
             members = []
             for tarinfo in tf:
                 # Get only files under the directory `self.dirname`
-                pathsplit = os.path.split(tarinfo.path)
+                pathsplit = os.path.normpath(tarinfo.path).split(os.sep)
                 if pathsplit[0] not in valid_paths:
                     print('WARNING: skipped file "%s" in archive; not in directory "%s"' %
                           (tarinfo.path, self.dirname))
                     continue
+                if len(pathsplit) == 1:
+                    continue
                 tarinfo.name = os.path.join(*pathsplit[1:])
                 members.append(tarinfo)
 
diff --git a/pyccc/tests/test_dir_refs.py b/pyccc/tests/test_dir_refs.py
index a30e4cc..827512b 100644
--- a/pyccc/tests/test_dir_refs.py
+++ b/pyccc/tests/test_dir_refs.py
@@ -84,3 +84,18 @@ def test_put_directory_reference_with_renaming(request, fixturename, tmpdir, rel
     assert not mismatch
     assert not errors
 
+
+def test_get_directory_with_subdirs(tmpdir):
+    engine = pyccc.Docker()
+
+    cmd = ("mkdir -p /opt/blah/fugu && echo a > /opt/blah/a"
+           " && echo b > /opt/blah/b && echo fish > /opt/blah/fugu/fish")
+
+    job = engine.launch(image='alpine',
+                        workingdir='/test',
+                        command=cmd)
+    job.wait()
+    outdir = job.get_directory('/opt/blah')
+    outdir.put(tmpdir)
+    for path in ['a', 'b', 'fugu/fish']:
+        assert os.path.exists(os.path.join(tmpdir, 'blah', path))