This is a workaround for: https://github.com/mybatis/spring/issues/58

FirstDatabaseConfig.java

@Configuration
public class FirstDatabaseConfig implements EnvironmentAware {
  private Environment env;
  
  @Override
  public void setEnvironment(final Environment env) {
    this.env = env;
  }
  
  @Bean
  public DataSource firstDataSource() {
    BasicDataSource source = new BasicDataSource();
    source.setDriverClassName(env.getRequiredProperty("first.dataSource.driverClassName");
    //and so on
    return source;
  }
  
  @Bean 
  public SqlSessionFactory firstSqlSessionFactory() throws Exception {
    SqlSessionFactoryBean bean = new SqlSessionFactoryBean();
    bean.setTypeAliasesPackage("org.example.model.first");
    bean.setDataSource(firstDataSource());
    return bean.getObject();
  }

  @Bean
  public MapperScannerConfigurer firstMapperScannerConfigurer() {
      MapperScannerConfigurer configurer = new MapperScannerConfigurer();
      configurer.setBasePackage("org.example.mapper.first");
      configurer.setSqlSessionFactoryBeanName("firstSqlSessionFactory");
      return configurer;
  }
}

SecondDatabaseConfig.java

@Configuration
public class SecondDatabaseConfig implements EnvironmentAware {
  private Environment env;
  
  @Override
  public void setEnvironment(final Environment env) {
    this.env = env;
  }
  
  @Bean
  public DataSource secondDataSource() {
    BasicDataSource source = new BasicDataSource();
    source.setDriverClassName(env.getRequiredProperty("second.dataSource.driverClassName");
    //and so on
    return source;
  }
  
  @Bean 
  public SqlSessionFactory secondSqlSessionFactory() throws Exception {
    SqlSessionFactoryBean bean = new SqlSessionFactoryBean();
    bean.setTypeAliasesPackage("org.example.model.second");
    bean.setDataSource(secondDataSource());
    return bean.getObject();
  }

  @Bean
  public MapperScannerConfigurer secondMapperScannerConfigurer() {
      MapperScannerConfigurer configurer = new MapperScannerConfigurer();
      configurer.setBasePackage("org.example.mapper.second");
      configurer.setSqlSessionFactoryBeanName("secondSqlSessionFactory");
      return configurer;
  }
}