diff --git a/pungi/metadata.py b/pungi/metadata.py
index 57cd05d5..4b886987 100644
--- a/pungi/metadata.py
+++ b/pungi/metadata.py
@@ -14,6 +14,7 @@
 # along with this program; if not, see <https://gnu.org/licenses/>.
 
 
+import copy
 import os
 import time
 import json
@@ -168,7 +169,18 @@ def write_compose_info(compose):
     compose.log_info("[BEGIN] %s" % msg)
 
     path = compose.paths.compose.metadata("composeinfo.json")
-    ci.dump(path)
+    # make a copy of composeinfo and modify the copy
+    # if any path in variant paths doesn't exist or just an empty
+    # dir, set it to None, then it won't be dumped.
+    ci_copy = copy.deepcopy(ci)
+    for variant in ci_copy.variants.variants.values():
+        for field in variant.paths._fields:
+            field_paths = getattr(variant.paths, field)
+            for arch, dirpath in field_paths.iteritems():
+                dirpath = os.path.join(compose.paths.compose.topdir(), dirpath)
+                if not (os.path.isdir(dirpath) and os.listdir(dirpath)):
+                    field_paths[arch] = None
+    ci_copy.dump(path)
 
     compose.log_info("[DONE ] %s" % msg)
 
diff --git a/pungi/phases/createiso.py b/pungi/phases/createiso.py
index 26609dbe..a0d7f425 100644
--- a/pungi/phases/createiso.py
+++ b/pungi/phases/createiso.py
@@ -66,6 +66,8 @@ class CreateisoPhase(PhaseLoggerMixin, PhaseBase):
 
         commands = []
         for variant in self.compose.get_variants(types=["variant", "layered-product", "optional"]):
+            if variant.is_empty:
+                continue
             for arch in variant.arches + ["src"]:
                 skip_iso = get_arch_variant_data(self.compose.conf, "createiso_skip", arch, variant)
                 if skip_iso == [True]:
diff --git a/pungi/phases/extra_files.py b/pungi/phases/extra_files.py
index 70284d97..6594c0d8 100644
--- a/pungi/phases/extra_files.py
+++ b/pungi/phases/extra_files.py
@@ -37,6 +37,8 @@ class ExtraFilesPhase(ConfigGuardedPhase):
     def run(self):
         for arch in self.compose.get_arches() + ["src"]:
             for variant in self.compose.get_variants(arch=arch):
+                if variant.is_empty:
+                    continue
                 cfg = get_arch_variant_data(self.compose.conf, self.name, arch, variant)
                 if cfg:
                     copy_extra_files(self.compose, cfg, arch, variant, self.pkgset_phase.package_sets)
diff --git a/pungi/phases/gather/__init__.py b/pungi/phases/gather/__init__.py
index 6b8da82d..8a22c4b3 100644
--- a/pungi/phases/gather/__init__.py
+++ b/pungi/phases/gather/__init__.py
@@ -75,6 +75,8 @@ class GatherPhase(PhaseBase):
 
         for arch in self.compose.get_arches():
             for variant in self.compose.get_variants(arch=arch):
+                if variant.is_empty:
+                    continue
                 link_files(self.compose, arch, variant,
                            pkg_map[arch][variant.uid],
                            self.pkgset_phase.package_sets,