diff --git a/meta/lib/bbconfigbuild/configfragments.py b/meta/lib/bbconfigbuild/configfragments.py
index fce3301bac9..34c6a3b4bcc 100644
--- a/meta/lib/bbconfigbuild/configfragments.py
+++ b/meta/lib/bbconfigbuild/configfragments.py
@@ -104,8 +104,11 @@ class ConfigFragmentsPlugin(LayerPlugin):
                   return True
         return False
 
+    def fragment_prefix(self, fragmentname):
+        return fragmentname.split("/",1)[0]
+
     def builtin_fragment_exists(self, fragmentname):
-        fragment_prefix = fragmentname.split("/",1)[0]
+        fragment_prefix = self.fragment_prefix(fragmentname)
         fragment_prefix_defs = set([f.split(':')[0] for f in self.tinfoil.config_data.getVar('OE_FRAGMENTS_BUILTIN').split()])
         return fragment_prefix in fragment_prefix_defs
 
@@ -128,6 +131,8 @@ class ConfigFragmentsPlugin(LayerPlugin):
                 if f in enabled_fragments:
                     print("Fragment {} already included in {}".format(f, args.confpath))
                 else:
+                    # first filter out all built-in fragments with the same prefix as the one that is being enabled
+                    enabled_fragments = [fragment for fragment in enabled_fragments if not(self.builtin_fragment_exists(fragment) and self.fragment_prefix(fragment) == self.fragment_prefix(f))]
                     enabled_fragments.append(f)
             return " ".join(enabled_fragments), None, 0, True
 
diff --git a/meta/lib/oeqa/selftest/cases/bblayers.py b/meta/lib/oeqa/selftest/cases/bblayers.py
index d82c5aaf376..7eb176aa04b 100644
--- a/meta/lib/oeqa/selftest/cases/bblayers.py
+++ b/meta/lib/oeqa/selftest/cases/bblayers.py
@@ -281,11 +281,11 @@ class BitbakeConfigBuild(OESelftestTestCase):
         2. Verify that SELFTEST_BUILTIN_FRAGMENT_VARIABLE is set after setting
            the fragment.
         3. Verify that SELFTEST_BUILTIN_FRAGMENT_VARIABLE is set after setting
-           the fragment with another value that overrides the first one.
-        4. Verify that SELFTEST_BUILTIN_FRAGMENT_VARIABLE is set to the previous
-           value after removing the second assignment (from step 3).
+           the fragment with another value that replaces the first one.
+        4. Repeat steps 2 and 3 to verify that going back and forth between values
+           works.
         5. Verify that SELFTEST_BUILTIN_FRAGMENT_VARIABLE is not set after
-           removing the original assignment.
+           removing the final assignment.
         """
         self.assertEqual(get_bb_var('SELFTEST_BUILTIN_FRAGMENT_VARIABLE'), None)
 
@@ -295,10 +295,13 @@ class BitbakeConfigBuild(OESelftestTestCase):
         runCmd('bitbake-config-build enable-fragment selftest-fragment/someothervalue')
         self.assertEqual(get_bb_var('SELFTEST_BUILTIN_FRAGMENT_VARIABLE'), 'someothervalue')
 
-        runCmd('bitbake-config-build disable-fragment selftest-fragment/someothervalue')
+        runCmd('bitbake-config-build enable-fragment selftest-fragment/somevalue')
         self.assertEqual(get_bb_var('SELFTEST_BUILTIN_FRAGMENT_VARIABLE'), 'somevalue')
 
-        runCmd('bitbake-config-build disable-fragment selftest-fragment/somevalue')
+        runCmd('bitbake-config-build enable-fragment selftest-fragment/someothervalue')
+        self.assertEqual(get_bb_var('SELFTEST_BUILTIN_FRAGMENT_VARIABLE'), 'someothervalue')
+
+        runCmd('bitbake-config-build disable-fragment selftest-fragment/someothervalue')
         self.assertEqual(get_bb_var('SELFTEST_BUILTIN_FRAGMENT_VARIABLE'), None)
 
     def test_show_fragment(self):