application.properties

datasource.mysql.url=jdbc:mysql://localhost:3306/mysql_demo
datasource.mysql.username=root
datasource.mysql.password=root

datasource.postgres.url=jdbc:postgresql://localhost:5432/postgres_demo
datasource.postgres.username=postgres
datasource.postgres.password=postgres

FirstConfiguration.java

@Configuration
@EnableJpaRepositories(basePackages = "io.eddumelendez.springdatajpa.repository1")
public class FirstConfiguration {

    @ConfigurationProperties(prefix = "datasource.postgres")
    @Bean
    @Primary
    public DataSource postgresDataSource() {
        return DataSourceBuilder.create().
                build();
    }

    @Bean(name = "entityManagerFactory")
    @Primary
    public LocalContainerEntityManagerFactoryBean emf1(EntityManagerFactoryBuilder builder){
        return builder
                .dataSource(postgresDataSource())
                .packages("io.eddumelendez.springdatajpa.domain1")
                .persistenceUnit("users")
                .build();
    }

}

SecondConfiguration.java

@Configuration
@EnableJpaRepositories(basePackages = "io.eddumelendez.springdatajpa.repository2", entityManagerFactoryRef = "emf2")
public class SecondConfiguration {

    @Bean
    @ConfigurationProperties(prefix = "datasource.mysql")
    public DataSource mysqlDataSource() {
        return DataSourceBuilder.create().build();
    }

    @Bean
    public LocalContainerEntityManagerFactoryBean emf2(EntityManagerFactoryBuilder builder){
        return builder
                .dataSource(mysqlDataSource())
                .packages("io.eddumelendez.springdatajpa.domain2")
                .persistenceUnit("customers")
                .build();
    }

}

Multiple datasources spring