diff --git a/pungi/phases/gather/sources/source_comps.py b/pungi/phases/gather/sources/source_comps.py
index 655c7673..447e0a47 100644
--- a/pungi/phases/gather/sources/source_comps.py
+++ b/pungi/phases/gather/sources/source_comps.py
@@ -39,7 +39,8 @@ class GatherSourceComps(pungi.phases.gather.source.GatherSourceBase):
 
         comps = CompsWrapper(self.compose.paths.work.comps(arch=arch))
 
-        if variant is not None and (variant.groups or variant.type != 'variant'):
+        is_modular = variant and not variant.groups and variant.modules
+        if variant is not None and (variant.groups or variant.type != 'variant' or is_modular):
             # Get packages for a particular variant. We want to skip the
             # filtering if the variant is top-level and has no groups (to use
             # all of them).
diff --git a/pungi/phases/init.py b/pungi/phases/init.py
index cbda4949..a01168a9 100644
--- a/pungi/phases/init.py
+++ b/pungi/phases/init.py
@@ -45,12 +45,16 @@ class InitPhase(PhaseBase):
 
             # write variant comps
             for variant in self.compose.get_variants():
+                is_modular = not variant.groups and variant.modules
                 for arch in variant.arches:
-                    if variant.groups or variant.type == 'optional':
+                    if variant.groups or variant.type == 'optional' or is_modular:
                         # The variant lists only some groups, run filter. Other
                         # option is that it's optional variant, in which case
                         # we want to filter everything (unless there was
                         # explicit list in which case it will be used).
+                        # For fully modular variant (one without groups but
+                        # with modules) we also want to filter (effectively
+                        # producing empty comps).
                         write_variant_comps(self.compose, arch, variant)
                     else:
                         # The variant does not mention any groups, copy
diff --git a/tests/test_initphase.py b/tests/test_initphase.py
index 7d8b639a..ae6c4e52 100644
--- a/tests/test_initphase.py
+++ b/tests/test_initphase.py
@@ -53,6 +53,7 @@ class TestInitPhase(PungiTestCase):
         compose = DummyCompose(self.topdir, {})
         compose.has_comps = True
         compose.variants['Everything'].groups = []
+        compose.variants['Everything'].modules = []
         phase = init.InitPhase(compose)
         phase.run()