How use more than one mongodb database in spring boot?

Yes, You can configure 2 databases in single spring-boot application. You have to add two database properties in single application.yml file.

#application.yml
        spring:
          data:
            mongodb:
              database: database_one
              uri: mongodb://root:[email protected]:27017/database_one
    # username : root, Password : root

        secondary:
          mongodb:
            database: database_two
            uri: mongodb://root:[email protected]:27017/database_two
    # username : root, Password : password

Then you have to add two database configuration files for spring and read these two properties in each file. For first database configuration file just add @Primary annotation for primary database properties. You can combine these two files in single as per your requirement.

@Configuration
public class DatabaseConfiguration {

    private static final Logger LOGGER = LoggerFactory.getLogger(DatabaseConfiguration.class);

    @Value("${spring.data.mongodb.uri}")
    private String mongoUri;

    @Value("${spring.data.mongodb.database}")
    private String mongoDbName;

    @Primary
    @Bean
    public MongoTemplate mongoTemplate() {    
        LOGGER.debug(" Instantiating MongoDbFactory ");
        SimpleMongoDbFactory mongoDbFactory = new SimpleMongoDbFactory(mongoClient(), mongoDbName);
            return new MongoTemplate(mongoDbFactory);
        }

    @Primary
    @Bean
    public MongoClient mongoClient() {
        return new MongoClient(mongoClientURI());
    }

    @Primary
    @Bean
    public MongoClientURI mongoClientURI() {
        LOGGER.debug(" creating connection with mongodb with uri [{}] ", mongoUri);
        return new MongoClientURI(mongoUri);
    }

}


# Second database configuration file.

@Configuration
public class SecondaryDatabaseConfiguration {

    private static final Logger LOGGER = LoggerFactory.getLogger(SecondaryDatabaseConfiguration.class);

    @Value("${secondary.mongodb.uri}")
    private String mongoUri;

    @Value("${secondary.mongodb.database}")
    private String mongoDbName ;

    @Bean(name = "mongoTemplateSecond")
    public MongoTemplate mongoTemplateSecondary() {
        LOGGER.debug(" Instantiating MongoDbFactory ");
        SimpleMongoDbFactory mongoDbFactory = new SimpleMongoDbFactory(mongoClientSecondary(), mongoDbName);
        return new MongoTemplate(mongoDbFactory);
    }

    @Bean
    public MongoClient mongoClientSecondary() {
        return new MongoClient(mongoClientURISecondary());
    }

    @Bean
    public MongoClientURI mongoClientURISecondary() {
        LOGGER.debug(" creating connection with mongodb with uri [{}] ", mongoUri);
        return new MongoClientURI(mongoUri);
    }
}

Then use @Qualifier annotation in your implementation class and pass bean name if you want to fetch from secondary database and for primary database you can directly Autowire.
@Qualifier annotation is used to differentiate beans of the same type.

    @Component
public class RepositoryImpl{

    @Qualifier(value = "mongoTemplateSecond")
    @Autowired
    MongoTemplate mongoTemplateSecond;   // for secondary database


    @Autowired
    private MongoTemplate mongoTemplate; // for primary database 


    public List<BasicDBObject> findRecordsInSecondary(Query query){
        List<BasicDBObject> basicDBObjects = mongoTemplateSecond.find(query, BasicDBObject.class, YOUR_COLLECTION_NAME);
        return basicDBObjects;
    }


    public List<BasicDBObject> findRecordsInPrimary(Query query){
        List<BasicDBObject> basicDBObjects = mongoTemplate.find(query, BasicDBObject.class, YOUR_COLLECTION_NAME);
        return basicDBObjects;
    }
}