diff --git a/mesonbuild/interpreter.py b/mesonbuild/interpreter.py
index a58e57d8a..1e225da7a 100644
--- a/mesonbuild/interpreter.py
+++ b/mesonbuild/interpreter.py
@@ -2269,7 +2269,10 @@ to directly access options of other subprojects.''')
         else:
             raise InterpreterException('Unknown backend "%s".' % backend)
 
-        self.coredata.init_backend_options(backend)
+        # Only init backend options on first invocation otherwise it would
+        # override values previously set from command line.
+        if self.environment.first_invocation:
+            self.coredata.init_backend_options(backend)
 
         options = {k: v for k, v in self.environment.cmd_line_options.items() if k.startswith('backend_')}
         self.coredata.set_options(options)
@@ -2289,9 +2292,16 @@ to directly access options of other subprojects.''')
             oi.process(self.option_file)
             self.coredata.merge_user_options(oi.options)
 
-        default_options = mesonlib.stringlistify(kwargs.get('default_options', []))
-        default_options = coredata.create_options_dict(default_options)
-        default_options.update(self.default_project_options)
+        # Do not set default_options on reconfigure otherwise it would override
+        # values previously set from command line. That means that changing
+        # default_options in a project will trigger a reconfigure but won't
+        # have any effect.
+        if self.environment.first_invocation:
+            default_options = mesonlib.stringlistify(kwargs.get('default_options', []))
+            default_options = coredata.create_options_dict(default_options)
+            default_options.update(self.default_project_options)
+        else:
+            default_options = {}
         self.set_options(default_options)
         self.set_backend()
 
diff --git a/run_unittests.py b/run_unittests.py
index f353a1080..7c68904ea 100755
--- a/run_unittests.py
+++ b/run_unittests.py
@@ -2117,6 +2117,11 @@ recommended as it is not supported on some platforms''')
         self.setconf('--default-library=shared')
         obj = mesonbuild.coredata.load(self.builddir)
         self.assertEqual(obj.builtins['default_library'].value, 'shared')
+        if self.backend is Backend.ninja:
+            # reconfigure target works only with ninja backend
+            self.build('reconfigure')
+            obj = mesonbuild.coredata.load(self.builddir)
+            self.assertEqual(obj.builtins['default_library'].value, 'shared')
         self.wipe()
 
         # Should fail on unknown options