diff --git a/fdroidserver/common.py b/fdroidserver/common.py
index 06284898..087dd431 100644
--- a/fdroidserver/common.py
+++ b/fdroidserver/common.py
@@ -1174,6 +1174,10 @@ class vcs:
     def initsubmodules(self):
         raise VCSException('Submodules not supported for this vcs type')
 
+    # Deinitialise and update submodules
+    def deinitsubmodules(self):
+        pass
+
     # Get a list of all known tags
     def gettags(self):
         if not self._gettags:
@@ -1338,6 +1342,12 @@ class vcs_git(vcs):
         if p.returncode != 0:
             raise VCSException(_("Git submodule update failed"), p.output)
 
+    def deinitsubmodules(self):
+        self.checkrepo()
+        p = FDroidPopen(['git', 'submodule', 'deinit', '--all'], cwd=self.local, output=False)
+        if p.returncode != 0:
+            raise VCSException(_("Git submodule deinit failed"), p.output)
+
     def _gettags(self):
         self.checkrepo()
         p = FDroidPopen(['git', 'tag'], cwd=self.local, output=False)
@@ -2188,6 +2198,8 @@ def prepare_source(vcs, app, build, build_dir, srclib_dir, extlib_dir, onserver=
     if build.submodules:
         logging.info(_("Initialising submodules"))
         vcs.initsubmodules()
+    else:
+        vcs.deinitsubmodules()
 
     # Check that a subdir (if we're using one) exists. This has to happen
     # after the checkout, since it might not exist elsewhere
diff --git a/tests/build.TestCase b/tests/build.TestCase
index 4a4c0001..cce6a424 100755
--- a/tests/build.TestCase
+++ b/tests/build.TestCase
@@ -586,6 +586,9 @@ class BuildTest(unittest.TestCase):
             def getsrclib(self):
                 return None
 
+            def deinitsubmodules(self):
+                pass
+
         # Test we trigger a scanner error without extlibs
         build.extlibs = []
         os.makedirs('build/libs')
diff --git a/tests/common.TestCase b/tests/common.TestCase
index 26cd979c..0fc8c41f 100755
--- a/tests/common.TestCase
+++ b/tests/common.TestCase
@@ -315,6 +315,9 @@ class CommonTest(unittest.TestCase):
             def getsrclib(self):
                 return None
 
+            def deinitsubmodules(self):
+                pass
+
         fdroidserver.common.prepare_source(FakeVcs(), app, build,
                                            fdroidclient_testdir, fdroidclient_testdir, fdroidclient_testdir)
 
@@ -385,6 +388,9 @@ class CommonTest(unittest.TestCase):
             def getsrclib(self):
                 return None
 
+            def deinitsubmodules(self):
+                pass
+
         fdroidserver.common.prepare_source(FakeVcs(), app, build,
                                            app_build_dir, srclib_testdir, app_build_dir,
                                            onserver=True, refresh=False)  # do not clone in this test