Multiple DataSources using Spring Data JDBC and CrudRepository Interface

I had a similar problem. My solution had to have my repositories put in 2 separate packages, as per Chris Savory answer, and then define 2 @Configuration classes defining 1 JdbcOperation each. Here's my full configuration (I have an SQL Server and an H2 data sources):

application.properties

Please note that these properties are Hikari CP specific. Mileage may vary if you chose a different CP (i.e. Tomcat)

## SQL SERVER DATA SOURCE
spring.sql-server-ds.jdbcUrl= jdbc:sqlserver://localhost:1554;databaseName=TestDB
spring.sql-server-ds.username= uteappl
spring.sql-server-ds.password= mypassword

## H2 DATA SOURCE
spring.h2-ds.jdbcUrl= jdbc:h2:mem:testdb;mode=MySQL
spring.h2-ds.username= sa
spring.h2-ds.password= password

First H2 @Configuration

@Configuration
@EnableJdbcRepositories(jdbcOperationsRef = "h2JdbcOperations", basePackages = "com.twinkie.repository.h2")
public class H2JdbcConfiguration extends AbstractJdbcConfiguration {


  @Bean
  @ConfigurationProperties(prefix = "spring.h2-ds")
  public DataSource h2DataSource() {
    return DataSourceBuilder.create().build();
  }


  @Bean
  NamedParameterJdbcOperations h2JdbcOperations(@Qualifier("h2DataSource") DataSource sqlServerDs) {
    return new NamedParameterJdbcTemplate(sqlServerDs);
  }

  @Bean
  public DataSourceInitializer h2DataSourceInitializer(
      @Qualifier("h2DataSource") final DataSource dataSource) {
    ResourceDatabasePopulator resourceDatabasePopulator = new ResourceDatabasePopulator(
        new ClassPathResource("schema.sql"));
    DataSourceInitializer dataSourceInitializer = new DataSourceInitializer();
    dataSourceInitializer.setDataSource(dataSource);
    dataSourceInitializer.setDatabasePopulator(resourceDatabasePopulator);
    return dataSourceInitializer;
  }
}

Second SQL Server @Configuration

@Configuration
@EnableJdbcRepositories("com.twinkie.repository.sqlserver")
public class SqlServerJdbcConfiguration {

  @Bean
  @Primary
  @ConfigurationProperties(prefix = "spring.sql-server-ds")
  public DataSource sqlServerDataSource() {
    return DataSourceBuilder.create().build();
  }

  @Bean
  @Primary
  NamedParameterJdbcOperations jdbcOperations(
      @Qualifier("sqlServerDataSource") DataSource sqlServerDs) {
    return new NamedParameterJdbcTemplate(sqlServerDs);
  }

}

Then I have my repositories (please note the different packages).

SQL Server

package com.twinkie.repository.sqlserver;

import com.twinkie.model.SoggettoAnag;
import java.util.List;
import org.springframework.data.jdbc.repository.query.Query;
import org.springframework.data.repository.CrudRepository;

public interface SoggettoAnagRepository extends CrudRepository<SoggettoAnag, Long> {

  @Query("SELECT * FROM LLA_SOGGETTO_ANAG WHERE sys_timestamp > :sysTimestamp ORDER BY sys_timestamp ASC")
  List<SoggettoAnag> findBySysTimestampGreaterThan(Long sysTimestamp);
}

H2

package com.twinkie.repository.h2;

import com.twinkie.model.GlSync;
import java.util.Optional;
import org.springframework.data.jdbc.repository.query.Modifying;
import org.springframework.data.jdbc.repository.query.Query;
import org.springframework.data.repository.Repository;

public interface GlSyncRepository extends Repository<GlSync, String> {

  @Modifying
  @Query("INSERT INTO GL_SYNC (table_name, last_rowversion) VALUES (:tableName, :rowVersion) ON DUPLICATE KEY UPDATE last_rowversion = :rowVersion")
  boolean save(String tableName, Long rowVersion);

  @Query("SELECT table_name, last_rowversion FROM gl_sync WHERE table_name = :tableName")
  Optional<GlSync> findById(String tableName);
}