diff --git a/src/fmu/dataio/dataio.py b/src/fmu/dataio/dataio.py
index 3b25124cd..6e740bb22 100644
--- a/src/fmu/dataio/dataio.py
+++ b/src/fmu/dataio/dataio.py
@@ -149,6 +149,9 @@ def _check_global_config(
                                 f"stratigraphy.{key}: 'alias' items must be strings\n"
                             )
 
+                    # After checking and warning, remove empty entries
+                    item["alias"] = list(filter(lambda i: i is not None, item["alias"]))
+
             if "stratigraphic_alias" in item:
                 if not isinstance(item["stratigraphic_alias"], list):
                     msg += f"stratigraphy.{key}: 'stratigraphic_alias' must be list.\n"
@@ -158,6 +161,11 @@ def _check_global_config(
                             msg += f"stratigraphy.{key}: 'stratigraphic_alias' items "
                             msg += "must be strings.\n"
 
+                    # After checking and warning, remove empty entries
+                    item["stratigraphic_alias"] = list(
+                        filter(lambda i: i is not None, item["stratigraphic_alias"])
+                    )
+
     if msg:
         if "err" in action:
             raise ValueError(msg)
diff --git a/tests/test_units/test_dataio.py b/tests/test_units/test_dataio.py
index 52c469b29..e4bb40026 100644
--- a/tests/test_units/test_dataio.py
+++ b/tests/test_units/test_dataio.py
@@ -79,17 +79,23 @@ def test_config_miss_required_fields(globalconfig1, regsurf):
         read_metadata(out)
 
 
-def test_config_stratigraphy_empty_entries_alias(globalconfig2):
-    """Test that empty entries in 'alias' is detected and warned."""
+def test_config_stratigraphy_empty_entries_alias(globalconfig2, regsurf):
+    """Test that empty entries in 'alias' is detected and warned and removed."""
     cfg = deepcopy(globalconfig2)
     cfg["stratigraphy"]["TopVolantis"]["alias"] += [None]
 
     with pytest.warns(PendingDeprecationWarning, match="'alias' items must be strings"):
-        ExportData(config=cfg, content="depth")
+        exp = ExportData(config=cfg, content="depth", name="TopVolantis")
+        metadata = exp.generate_metadata(regsurf)
+
+    assert None not in metadata["data"]["alias"]
+
+
+def test_config_stratigraphy_empty_entries_stratigraphic_alias(globalconfig2, regsurf):
+    """Test that empty entries in 'stratigraphic_alias' detected and warned."""
 
+    # Note! stratigraphic_alias is not implemented, but we still check consistency
 
-def test_config_stratigraphy_empty_entries_stratigraphic_alias(globalconfig2):
-    """Test that empty entries in 'stratigraphic_alias' is detected and warned."""
     cfg = deepcopy(globalconfig2)
     cfg["stratigraphy"]["TopVolantis"]["stratigraphic_alias"] += [None]