diff --git a/nf_core/modules/lint/module_changes.py b/nf_core/modules/lint/module_changes.py
index b6e9978198..74e5df064e 100644
--- a/nf_core/modules/lint/module_changes.py
+++ b/nf_core/modules/lint/module_changes.py
@@ -24,7 +24,8 @@ def module_changes(module_lint_object, module):
     if module.is_patched:
         # If the module is patched, we need to apply
         # the patch in reverse before comparing with the remote
-        tempdir = Path(tempfile.mkdtemp())
+        tempdir_parent = Path(tempfile.mkdtemp())
+        tempdir = tempdir_parent / "tmp_module_dir"
         shutil.copytree(module.module_dir, tempdir)
         try:
             new_lines = ModulesDiffer.try_apply_patch(
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index 64b5f2ff0f..d5793dfd05 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -1,8 +1,11 @@
+import os
+
 import pytest
 
 import nf_core.modules
 
 from ..utils import GITLAB_URL
+from .patch import BISMARK_ALIGN, PATCH_BRANCH, setup_patch
 
 
 def test_modules_lint_trimgalore(self):
@@ -48,3 +51,26 @@ def test_modules_lint_gitlab_modules(self):
     assert len(module_lint.failed) == 0
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
+
+
+def test_modules_lint_patched_modules(self):
+    """
+    Test creating a patch file and applying it to a new version of the the files
+    """
+    setup_patch(self.pipeline_dir, True)
+
+    # Create a patch file
+    patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
+    patch_obj.patch(BISMARK_ALIGN)
+
+    # change temporarily working directory to the pipeline directory
+    # to avoid error from try_apply_patch() during linting
+    wd_old = os.getcwd()
+    os.chdir(self.pipeline_dir)
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+    module_lint.lint(print_results=False, all_modules=True)
+    os.chdir(wd_old)
+
+    assert len(module_lint.failed) == 0
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
diff --git a/tests/test_modules.py b/tests/test_modules.py
index c8dbf948f3..52ca197bd7 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -115,6 +115,7 @@ def test_modulesrepo_class(self):
         test_modules_lint_gitlab_modules,
         test_modules_lint_new_modules,
         test_modules_lint_no_gitlab,
+        test_modules_lint_patched_modules,
         test_modules_lint_trimgalore,
     )
     from .modules.list import (