diff --git a/augur/filter/subsample.py b/augur/filter/subsample.py
index 3d62a2639..b39ee6228 100644
--- a/augur/filter/subsample.py
+++ b/augur/filter/subsample.py
@@ -45,11 +45,6 @@ def get_valid_group_by_columns(metadata_columns: Set[str], group_by: List[str])
             raise AugurError(f"{constants.DATE_MONTH_COLUMN!r} and {constants.DATE_WEEK_COLUMN!r} grouping cannot be used together.")
 
     if generated_columns_requested:
-
-        for col in sorted(generated_columns_requested):
-            if col in metadata_columns:
-                print_err(f"WARNING: `--group-by {col}` uses a generated {col} value from the {METADATA_DATE_COLUMN!r} column. The custom '{col}' column in the metadata is ignored for grouping purposes.")
-
         if METADATA_DATE_COLUMN not in metadata_columns:
             print_err(f"WARNING: A {METADATA_DATE_COLUMN!r} column could not be found to group-by {sorted(generated_columns_requested)}.")
             print_err(f"Filtering by group may behave differently than expected!")
@@ -375,6 +370,10 @@ def create_grouping_table(group_by_columns: List[str], metadata_columns: Set[str
                 # Add an extra comma for valid SQL.
                 + ',')
 
+            for column in sorted(generated_group_by_columns):
+                if column in metadata_columns:
+                    print_err(f"WARNING: `--group-by {column}` uses a generated {column} value from the {METADATA_DATE_COLUMN!r} column. The custom '{column}' column in the metadata is ignored for grouping purposes.")
+
         metadata_group_by_columns = group_by_columns_set - generated_group_by_columns
 
         if metadata_group_by_columns: