Here is a sample.    
//This is like a base class for all your mongoconfigs.   
    public class MongoConfig  {
    private static final Logger LOG = LoggerFactory.getLogger(MongoConfig.class);
    @NoArgsConstructor
    @Getter
    @Setter
    class MongoDbProperties{
        private String host;
        private int port;
        private String dbName;
        private String dbUser;
        private String dbPwd;
    }
    Mongo createMongoClient(ServerAddress serverAddress, MongoCredential... credentials) {
        if (credentials != null && credentials.length > 0) {
            final List<MongoCredential> credentialList = new ArrayList<>();
            credentialList.addAll(Arrays.asList(credentials));
            LOG.info("Creating connection with credentials: " + credentialList);
            return new MongoClient(serverAddress, credentialList;
        } else {
            return new MongoClient(serverAddress);
        }
    }
    Mongo getMongoClient(MongoDbProperties mongoDbProperties) {
        LOG.info("Initializing mongo client for {}. Host={}, Port={} ", mongoDbProperties.getDbName(), mongoDbProperties.getHost(), mongoDbProperties.getPort());
        Mongo mongoClient;
        if(!mongoDbProperties.getDbUser().isEmpty() && !mongoDbProperties.getDbPwd().isEmpty()) {
            MongoCredential credential = MongoCredential.createCredential(mongoDbProperties.getDbUser(), mongoDbProperties.getDbName(), mongoDbProperties.getDbPwd().toCharArray());
            mongoClient = createMongoClient(new ServerAddress(mongoDbProperties.getHost(), mongoDbProperties.getPort()), credential);
        }
        else
            mongoClient = createMongoClient(new ServerAddress(mongoDbProperties.getHost(), mongoDbProperties.getPort()));
        LOG.info("Initializing mongo template for products dataBase={} ", mongoDbProperties.getDbName());
        return mongoClient;
    }
    @Bean
    @ConfigurationProperties(prefix = "mongo.default")
    public MongoOptionsProperties defaultMongoOptionsProperties() {
        return new MongoOptionsProperties();
    }
 }
Then have as many config files as mongo databases you want to connect to like these:  
@Configuration
@EnableMongoRepositories(basePackages = "com.product.repository.shop.swiss", mongoTemplateRef = "swissMongoProductTemplate")
class SWissProductMongoConfig extends MongoConfig {
    @Bean(name = "swissMongoProductTemplate")
    public MongoTemplate swissMongoProductTemplate() throws Exception {
        MongoDbProperties mongoDbProperties = shopSWissProductMongoProperties();
        Mongo mongoClient = getMongoClient(mongoDbProperties);
        return new MongoTemplate(mongoClient, mongoDbProperties.getDbName());
    }
        @Bean
        @ConfigurationProperties(prefix = "mongo.product.swiss")
        public MongoDbProperties shopSWissProductMongoProperties(){
            return new MongoDbProperties();
        }
    }
and
@Configuration
@EnableMongoRepositories(basePackages = "com.product.repository.shop.france", mongoTemplateRef = "franceMongoProductTemplate")
class SWissProductMongoConfig extends MongoConfig {
    @Bean(name = "franceMongoProductTemplate")
    public MongoTemplate franceMongoProductTemplate() throws Exception {
        MongoDbProperties mongoDbProperties = shopFranceProductMongoProperties();
        Mongo mongoClient = getMongoClient(mongoDbProperties);
        return new MongoTemplate(mongoClient, mongoDbProperties.getDbName());
    }
    @Bean
    @ConfigurationProperties(prefix = "mongo.product.france")
    public MongoDbProperties shopFranceProductMongoProperties() {
        return new MongoDbProperties();
    }
}
Have something like this in your yml 
mongo:
  product:
    france :
      dbName: 
      host: 
      port: 
      dbUser:
      dbPwd:
    swiss:
      dbName: 
      host: 
      port: 
      dbUser: 
      dbPwd: 
Make sure you have the repository classes in the packages mentioned in the basePackages attribute of annotaion EnableMongoRepositories