diff --git a/mesonbuild/options.py b/mesonbuild/options.py
index 0ada8432c842..3ed0c7eb659f 100644
--- a/mesonbuild/options.py
+++ b/mesonbuild/options.py
@@ -909,12 +909,10 @@ def add_system_option_internal(self, key: OptionKey, valobj: AnyOptionType) -> N
         if key.subproject:
             proj_key = key.evolve(subproject=None)
             self.add_system_option_internal(proj_key, valobj)
-            if pval is not None:
-                self.augments[key] = pval
         else:
             self.options[key] = valobj
-            if pval is not None:
-                self.set_option(key, pval)
+        if pval is not None:
+            self.set_option(key, pval)
 
     def add_compiler_option(self, language: str, key: T.Union[OptionKey, str], valobj: AnyOptionType) -> None:
         key = self.ensure_and_validate_key(key)
diff --git a/unittests/optiontests.py b/unittests/optiontests.py
index 8f49a804e59d..7273ecf47f04 100644
--- a/unittests/optiontests.py
+++ b/unittests/optiontests.py
@@ -474,3 +474,21 @@ def test_deprecated_nonstring_value(self):
         optstore.set_option(OptionKey(name), True)
         value = optstore.get_value(name)
         self.assertEqual(value, '1')
+
+    def test_pending_augment_validation(self):
+        name = 'b_lto'
+        subproject = 'mysubproject'
+
+        optstore = OptionStore(False)
+        prefix = UserStringOption('prefix', 'This is needed by OptionStore', '/usr')
+        optstore.add_system_option('prefix', prefix)
+
+        optstore.initialize_from_top_level_project_call({}, {}, {})
+        optstore.initialize_from_subproject_call(subproject, {}, {OptionKey(name): 'true'}, {}, {})
+
+        bo = UserBooleanOption(name, 'LTO', False)
+        key = OptionKey(name, subproject=subproject)
+        optstore.add_system_option(key, bo)
+        stored_value = optstore.get_value_for(key)
+        self.assertIsInstance(stored_value, bool)
+        self.assertTrue(stored_value)