Right now, I can manually add a native directory for autolinking using the expo.nativeModulesDir entry in package.json . However, this autolinks every module in the directory. There is normally an option (for expo modules only) to exclude modules using the expo.exclude entry in package.json . Based on this code, it seems that this is arbitrarily not allowed for custom native modules. ( https://github.com/expo/expo/blob/main/packages/expo-modules-autolinking/src/autolinking/findModules.ts#L54-L60 ) This means that there is no way currently to selectively prevent custom native modules from being included, as react-native.config.js is not respected by expo autolinking.