diff --git a/commands/daemon/settings.go b/commands/daemon/settings.go
index 151ce9da61a..2d8b9ca9039 100644
--- a/commands/daemon/settings.go
+++ b/commands/daemon/settings.go
@@ -79,9 +79,13 @@ func (s *ArduinoCoreServerImpl) SettingsMerge(ctx context.Context, req *rpc.Sett
 	// Set each value individually.
 	// This is done because Viper ignores empty strings or maps when
 	// using the MergeConfigMap function.
+	updatedSettings := configuration.Init("")
 	for k, v := range mapped {
-		configuration.Settings.Set(k, v)
+		updatedSettings.Set(k, v)
 	}
+	configPath := configuration.Settings.ConfigFileUsed()
+	updatedSettings.SetConfigFile(configPath)
+	configuration.Settings = updatedSettings
 
 	return &rpc.SettingsMergeResponse{}, nil
 }
diff --git a/commands/daemon/settings_test.go b/commands/daemon/settings_test.go
index c5366e179b5..93f49174e50 100644
--- a/commands/daemon/settings_test.go
+++ b/commands/daemon/settings_test.go
@@ -81,6 +81,13 @@ func TestMerge(t *testing.T) {
 	require.Equal(t, "", configuration.Settings.GetString("foo"))
 	require.Equal(t, false, configuration.Settings.GetBool("sketch.always_export_binaries"))
 
+	bulkSettings = `{"network": {}}`
+	res, err = svc.SettingsMerge(context.Background(), &rpc.SettingsMergeRequest{JsonData: bulkSettings})
+	require.NotNil(t, res)
+	require.NoError(t, err)
+
+	require.Equal(t, "", configuration.Settings.GetString("proxy"))
+
 	reset()
 }
 
@@ -113,6 +120,8 @@ func TestGetMergedValue(t *testing.T) {
 	res, err = svc.SettingsGetValue(context.Background(), key)
 	require.NoError(t, err)
 	require.Equal(t, `"bar"`, res.GetJsonData())
+
+	reset()
 }
 
 func TestGetValueNotFound(t *testing.T) {