diff --git a/CHANGELOG.md b/CHANGELOG.md
index d3f399c08..d634acea8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -49,6 +49,9 @@
 * Added `--conda-package-version` flag for specifying version of conda package in `nf-core modules create`. ([#1238](https://github.com/nf-core/tools/issues/1238))
 * Add option of writing diffs to file in `nf-core modules update` using either interactive prompts or the new `--diff-file` flag.
 * Fixed edge case where module names that were substrings of other modules caused both to be installed ([#1380](https://github.com/nf-core/tools/issues/1380))
+* Tweak handling of empty files when generating the test YAML ([#1376](https://github.com/nf-core/tools/issues/1376))
+    * Fail linting if a md5sum for an empty file is found (instead of a warning)
+    * Don't skip the md5 when generating a test file if an empty file is found (so that linting fails and can be manually checked)
 
 ## [v2.2 - Lead Liger](https://github.com/nf-core/tools/releases/tag/2.2) - [2021-12-14]
 
diff --git a/nf_core/modules/lint/module_tests.py b/nf_core/modules/lint/module_tests.py
index 7bef0112d..a8470d0d1 100644
--- a/nf_core/modules/lint/module_tests.py
+++ b/nf_core/modules/lint/module_tests.py
@@ -55,7 +55,7 @@ def module_tests(module_lint_object, module):
                 # Look for md5sums of empty files
                 for tfile in test.get("files", []):
                     if tfile.get("md5sum") == "d41d8cd98f00b204e9800998ecf8427e":
-                        module.warned.append(
+                        module.failed.append(
                             (
                                 "test_yml_md5sum",
                                 "md5sum for empty file found: d41d8cd98f00b204e9800998ecf8427e",
@@ -63,7 +63,7 @@ def module_tests(module_lint_object, module):
                             )
                         )
                     if tfile.get("md5sum") == "7029066c27ac6f5ef18d660d5741979a":
-                        module.warned.append(
+                        module.failed.append(
                             (
                                 "test_yml_md5sum",
                                 "md5sum for compressed empty file found: 7029066c27ac6f5ef18d660d5741979a",
diff --git a/nf_core/modules/test_yml_builder.py b/nf_core/modules/test_yml_builder.py
index 5bfe2365c..d210cf350 100644
--- a/nf_core/modules/test_yml_builder.py
+++ b/nf_core/modules/test_yml_builder.py
@@ -232,10 +232,12 @@ def create_test_file_dict(self, results_dir, is_repeat=False):
                 # Check that this isn't an empty file
                 if self.check_if_empty_file(elem):
                     if not is_repeat:
-                        self.errors.append(f"Empty file, skipping md5sum: '{os.path.basename(elem)}'")
-                else:
-                    elem_md5 = self._md5(elem)
-                    test_file["md5sum"] = elem_md5
+                        self.errors.append(f"Empty file found! '{os.path.basename(elem)}'")
+                # Add the md5 anyway, linting should fail later and can be manually removed if needed.
+                #  Originally we skipped this if empty, but then it's too easy to miss the warning.
+                #  Equally, if a file is legitimately empty we don't want to prevent this from working.
+                elem_md5 = self._md5(elem)
+                test_file["md5sum"] = elem_md5
                 # Switch out the results directory path with the expected 'output' directory
                 test_file["path"] = elem.replace(results_dir, "output")
                 test_files.append(test_file)