spring.datasource.url=jdbc:h2:mem
spring.datasource.username=
spring.datasource.password=
spring.datasource.driver-class-name=org.h2.Driver

another.datasource.url=jdbc:mysql://localhost:3306/test
another.datasource.username=root
another.datasource.password=
another.datasource.hibernate.dialect=org.hibernate.dialect.MySQL5Dialect
another.datasource.driverClassName=com.mysql.jdbc.Driver

@Configuration
@EnableTransactionManagement
@EnableJpaRepositories(
        entityManagerFactoryRef = "anotherEntityManagerFactory",
        transactionManagerRef = "anotherTransactionManager",
        basePackages = {"test.repository.mysql"})
public class RepositoryConfig {

    @Autowired
    JpaVendorAdapter jpaVendorAdapter;

    @Value("${another.datasource.url}")
    private String databaseUrl;

    @Value("${another.datasource.username}")
    private String username;

    @Value("${another.datasource.password}")
    private String password;

    @Value("${another.datasource.driverClassName}")
    private String driverClassName;

    public DataSource dataSource() {
        DriverManagerDataSource dataSource = new DriverManagerDataSource(databaseUrl, username, password);
        dataSource.setDriverClassName(driverClassName);
        return dataSource;
    }

    @Bean(name = "anotherEntityManager")
    public EntityManager entityManager() {
        return entityManagerFactory().createEntityManager();
    }

    @Bean(name = "anotherEntityManagerFactory")
    public EntityManagerFactory entityManagerFactory() {
        Properties properties = new Properties();
        LocalContainerEntityManagerFactoryBean emf = new LocalContainerEntityManagerFactoryBean();
        emf.setDataSource(dataSource());
        emf.setJpaVendorAdapter(jpaVendorAdapter);
        emf.setPackagesToScan("test.entity.mysql");   // <- package for entities
        emf.setPersistenceUnitName("anotherEntity");
        emf.setJpaProperties(properties);
        emf.afterPropertiesSet();
        return emf.getObject();
    }

    @Bean(name = "anotherTransactionManager")
    public PlatformTransactionManager transactionManager() {
        return new JpaTransactionManager(entityManagerFactory());
    }
}

@Bean
public LocalContainerEntityManagerFactoryBean customerEntityManagerFactory(
        EntityManagerFactoryBuilder builder) {
    return builder
            .dataSource(customerDataSource())
            .packages(Customer.class)
            .persistenceUnit("customers")
            .build();
}

@Bean
public LocalContainerEntityManagerFactoryBean orderEntityManagerFactory(
        EntityManagerFactoryBuilder builder) {
    return builder
            .dataSource(orderDataSource())
            .packages(Order.class)
            .persistenceUnit("orders")
            .build();
}

@Configuration
@EnableJpaRepositories(basePackageClasses = Customer.class,
        entityManagerFactoryRef = "customerEntityManagerFactory")
public class CustomerConfiguration {
    ...
}

@Configuration
@EnableJpaRepositories(basePackageClasses = Order.class,
        entityManagerFactoryRef = "orderEntityManagerFactory")
public class OrderConfiguration {
    ...
}

@Bean(name = "mysql")
@Primary
@ConfigurationProperties(prefix="datasource.mysql")
public DataSourceProperties fooDataSourceProperties() {
     return DataSourceBuilder
             .create()
             .build();
}

@Bean(name = "postgres")
public DataSource fooDataSource() {
    return fooDataSourceProperties().initializeDataSourceBuilder().build();
}