diff --git a/pungi/phases/pkgset/sources/source_koji.py b/pungi/phases/pkgset/sources/source_koji.py
index 2ca22db0..23cc09e1 100644
--- a/pungi/phases/pkgset/sources/source_koji.py
+++ b/pungi/phases/pkgset/sources/source_koji.py
@@ -23,6 +23,13 @@ from itertools import groupby
 
 from kobo.rpmlib import parse_nvra
 from kobo.shortcuts import force_list
+from typing import (
+    Dict,
+    AnyStr,
+    List,
+    Tuple,
+    Set,
+)
 
 import pungi.wrappers.kojiwrapper
 from pungi.wrappers.comps import CompsWrapper
@@ -507,6 +514,45 @@ def filter_by_whitelist(compose, module_builds, input_modules, expected_modules)
     return modules_to_keep
 
 
+def _filter_expected_modules(
+        variant_name: AnyStr,
+        variant_arches: List[AnyStr],
+        expected_modules: Set[AnyStr],
+        filtered_modules: List[Tuple[AnyStr, Dict[AnyStr, List[AnyStr]]]],
+) -> set:
+    """
+    Function filters out all modules which are listed in Pungi config.
+    Those modules can be absent in koji env so we must remove it from
+    the expected modules list otherwise Pungi will fail
+    """
+    for variant_regexp, filters_dict in filtered_modules:
+        for arch, modules in filters_dict.items():
+            arch = '.*' if arch == '*' else arch
+            variant_regexp = '.*' if variant_regexp == '*' else variant_regexp
+            modules = ['.*' if module == '*' else module for module in modules]
+            cond1 = re.findall(
+                variant_regexp,
+                variant_name,
+            )
+            cond2 = any(
+                re.findall(
+                    arch,
+                    variant_arch,
+                ) for variant_arch in variant_arches
+            )
+            if cond1 and cond2:
+                expected_modules = {
+                    expected_module for expected_module in expected_modules if
+                    not all(
+                        re.findall(
+                            filtered_module,
+                            expected_module,
+                        ) for filtered_module in modules
+                    )
+                }
+    return expected_modules
+
+
 def _get_modules_from_koji_tags(
     compose, koji_wrapper, event_id, variant, variant_tags, tag_to_mmd
 ):
@@ -622,7 +668,12 @@ def _get_modules_from_koji_tags(
                 # needed in createrepo phase where metadata is exposed by
                 # productmd
                 variant.module_uid_to_koji_tag[nsvc] = module_tag
-
+    expected_modules = _filter_expected_modules(
+        variant_name=variant.name,
+        variant_arches=variant.arches,
+        expected_modules=expected_modules,
+        filtered_modules=compose.conf['filter_modules'],
+    )
     if expected_modules:
         # There are some module names that were listed in configuration and not
         # found in any tag...
diff --git a/tests/test_pkgset_source_koji.py b/tests/test_pkgset_source_koji.py
index 8d72a608..9d844bc6 100644
--- a/tests/test_pkgset_source_koji.py
+++ b/tests/test_pkgset_source_koji.py
@@ -1,15 +1,19 @@
 # -*- coding: utf-8 -*-
 
 import json
-import mock
+
 import os
 import re
 import six
+from ddt import ddt, data, unpack
+from typing import AnyStr, List, Set, Dict, Tuple
 
 try:
     import unittest2 as unittest
+    from unittest2 import mock
 except ImportError:
     import unittest
+    from unittest import mock
 
 from pungi.phases.pkgset.sources import source_koji
 from tests import helpers
@@ -968,3 +972,124 @@ class TestAddScratchModuleToVariant(helpers.PungiTestCase):
         self.compose.log_warning.assert_called_once_with(
             "Only test composes could include scratch module builds"
         )
+
+
+@ddt
+class TestSourceKoji(unittest.TestCase):
+
+    @unpack
+    @data(
+        (
+            'AppStream',
+            [
+                'x86_64',
+                'i386'
+            ],
+            {
+                'python39-devel:3.9',
+                'python39:3.9',
+            },
+            [
+                (
+                    '^(BaseOS|AppStream|PowerTools)$',
+                    {
+                        'x86_64': [
+                            'python39:3.9',
+                        ],
+                        'aarch64': [
+                            'python39-devel:3.9',
+                        ]
+                    }
+                )
+            ],
+            {
+                'python39-devel:3.9',
+            }
+        ),
+        (
+            'AppStream',
+            [
+                'x86_64',
+                'i386'
+            ],
+            {
+                'python39-devel:3.9',
+                'python39:3.9',
+                'python38-devel:3.8',
+                'python38:3.8',
+            },
+            [
+                (
+                    '^(BaseOS|AppStream|PowerTools)$',
+                    {
+                        'x86_64': [
+                            'python39:3.9',
+                        ],
+                        '*': [
+                            'python38-devel:3.8',
+                        ]
+                    }
+                )
+            ],
+            {
+                'python39-devel:3.9',
+                'python38:3.8',
+            }
+        ),
+        (
+            'AppStream',
+            [
+                'x86_64',
+                'i386'
+            ],
+            {
+                'python39-devel:3.9',
+                'python39:3.9',
+                'python38-devel:3.8',
+                'python38:3.8',
+            },
+            [
+                (
+                    '^(BaseOS|AppStream|PowerTools)$',
+                    {
+                        'x86_64': [
+                            'python39:3.9',
+                        ],
+                        'aarch64': [
+                            'python38-devel:3.8',
+                        ]
+                    }
+                ),
+                (
+                    '*',
+                    {
+                        '*': [
+                            'python38-devel:3.8',
+                        ]
+                    }
+                ),
+            ],
+            {
+                'python39-devel:3.9',
+                'python38:3.8',
+            }
+        ),
+    )
+    def test__filter_expected_modules(
+            self,
+            variant_name: AnyStr,
+            variant_arches: List[AnyStr],
+            expected_modules: Set[AnyStr],
+            filtered_modules: List[Tuple[AnyStr, Dict[AnyStr, List[AnyStr]]]],
+            expected_result: Set[AnyStr],
+    ) -> None:
+        real_result = source_koji._filter_expected_modules(
+            variant_name=variant_name,
+            variant_arches=variant_arches,
+            expected_modules=expected_modules,
+            filtered_modules=filtered_modules,
+        )
+        self.assertSetEqual(
+            real_result,
+            expected_result,
+        )
\ No newline at end of file