You could use something similar that's done by mongeez. This is basically a starter for spring-boot that runs scripts before spring-data-mongodb beans are initialized.

You could tag along and leverage spring-boot's initialization lifecycle, where after wiring the beans, it executes all CommandLineRunner beans.

@SpringBootApplication
public class YourApplication {
    final Logger logger = LoggerFactory.getLogger(getClass());

    @Autowired
    private MongoRepository repo;

    @Bean
    CommandLineRunner preLoadMongo() throws Exception {
        return args -> {
            //repo.doSOmethingInMongoDB
       }

    public static void main(String[] args) {
        SpringApplication.run(YourApplication.class, args);
    }