diff --git a/rhodecode/lib/middleware/simplevcs.py b/rhodecode/lib/middleware/simplevcs.py
--- a/rhodecode/lib/middleware/simplevcs.py
+++ b/rhodecode/lib/middleware/simplevcs.py
@@ -230,7 +230,8 @@ class SimpleVCS(object):
                 repo_name, db_repo.repo_type, scm_type)
             return False
 
-        return is_valid_repo(repo_name, base_path, explicit_scm=scm_type)
+        return is_valid_repo(repo_name, base_path,
+                             explicit_scm=scm_type, expect_scm=scm_type)
 
     def valid_and_active_user(self, user):
         """
diff --git a/rhodecode/lib/utils.py b/rhodecode/lib/utils.py
--- a/rhodecode/lib/utils.py
+++ b/rhodecode/lib/utils.py
@@ -260,7 +260,7 @@ def is_valid_repo(repo_name, base_path, 
 
     try:
         if explicit_scm:
-            detected_scms = [get_scm_backend(explicit_scm)]
+            detected_scms = [get_scm_backend(explicit_scm)(full_path).alias]
         else:
             detected_scms = get_scm(full_path)
 
diff --git a/rhodecode/tests/other/vcs_operations/test_vcs_operations.py b/rhodecode/tests/other/vcs_operations/test_vcs_operations.py
--- a/rhodecode/tests/other/vcs_operations/test_vcs_operations.py
+++ b/rhodecode/tests/other/vcs_operations/test_vcs_operations.py
@@ -39,6 +39,7 @@ from rhodecode.lib.vcs.nodes import File
 from rhodecode.model.auth_token import AuthTokenModel
 from rhodecode.model.db import Repository, UserIpMap, CacheKey
 from rhodecode.model.meta import Session
+from rhodecode.model.repo import RepoModel
 from rhodecode.model.user import UserModel
 from rhodecode.tests import (GIT_REPO, HG_REPO, TEST_USER_ADMIN_LOGIN)
 
@@ -177,6 +178,28 @@ class TestVCSOperations(object):
             'git clone', clone_url, tmpdir.strpath)
         assert 'not found' in stderr
 
+    def test_clone_non_existing_store_path_hg(self, rc_web_server, tmpdir, user_util):
+        repo = user_util.create_repo()
+        clone_url = rc_web_server.repo_clone_url(repo.repo_name)
+
+        # Damage repo by removing it's folder
+        RepoModel()._delete_filesystem_repo(repo)
+
+        stdout, stderr = Command('/tmp').execute(
+            'hg clone', clone_url, tmpdir.strpath)
+        assert 'HTTP Error 404: Not Found' in stderr
+
+    def test_clone_non_existing_store_path_git(self, rc_web_server, tmpdir, user_util):
+        repo = user_util.create_repo(repo_type='git')
+        clone_url = rc_web_server.repo_clone_url(repo.repo_name)
+
+        # Damage repo by removing it's folder
+        RepoModel()._delete_filesystem_repo(repo)
+
+        stdout, stderr = Command('/tmp').execute(
+            'git clone', clone_url, tmpdir.strpath)
+        assert 'not found' in stderr
+
     def test_push_new_file_hg(self, rc_web_server, tmpdir):
         clone_url = rc_web_server.repo_clone_url(HG_REPO)
         stdout, stderr = Command('/tmp').execute(