diff --git a/niworkflows/utils/spaces.py b/niworkflows/utils/spaces.py
index fc5e93e4dff..09a2b84bdf2 100644
--- a/niworkflows/utils/spaces.py
+++ b/niworkflows/utils/spaces.py
@@ -708,11 +708,17 @@ def __call__(self, parser, namespace, values, option_string=None):
         if not values:
             # option was called without any output spaces, so user does not want outputs
             spaces.checkpoint()
+
+        invalid_spaces = []
         for val in values:
             val = val.rstrip(':')
+            space = val.split(':', 1)[0]
+            if space in NONSTANDARD_REFERENCES and ':' in val:
+                invalid_spaces.append(val)
+
             if (
-                val not in NONSTANDARD_REFERENCES
-                and not val.split(':')[0].startswith('fs')
+                space not in NONSTANDARD_REFERENCES
+                and not space.startswith('fs')
                 and ':res-' not in val
                 and ':resolution-' not in val
             ):
@@ -721,8 +727,16 @@ def __call__(self, parser, namespace, values, option_string=None):
                 # https://github.com/nipreps/niworkflows/pull/457#discussion_r375510227
                 # https://github.com/nipreps/niworkflows/pull/494
                 val = f'{val}:res-native'
+
             for sp in Reference.from_string(val):
                 spaces.add(sp)
+
+        if invalid_spaces:
+            raise ValueError(
+                'Modifiers are not allowed for nonstandard spaces. '
+                f'Invalid space(s): {", ".join(invalid_spaces)}'
+            )
+
         setattr(namespace, self.dest, spaces)
 
 
diff --git a/niworkflows/utils/tests/test_spaces.py b/niworkflows/utils/tests/test_spaces.py
index 1f37c56b778..ae9c4644be0 100644
--- a/niworkflows/utils/tests/test_spaces.py
+++ b/niworkflows/utils/tests/test_spaces.py
@@ -104,3 +104,16 @@ def test_space_action_edgecases(parser, flag, expected):
     pargs = parser.parse_known_args(flag)[0]
     spaces = pargs.spaces
     assert spaces.is_cached() is expected
+
+
+@pytest.mark.parametrize(
+    ('spaces', 'expected'),
+    [
+        (('func:res-01',), 'Modifiers are not allowed for nonstandard spaces.'),
+        (('anat:den-91k',), 'Modifiers are not allowed for nonstandard spaces.'),
+        (('shouldraise',), 'space identifier "shouldraise" is invalid.'),
+    ],
+)
+def test_space_action_invalid_spaces(parser, spaces, expected):
+    with pytest.raises(ValueError, match=expected):
+        parser.parse_known_args(args=('--spaces',) + spaces)[0]