Multiple datasources migrations using Flyway in a Spring Boot application

Flyway supports migrations coded within Java and so you can start Flyway during your application startup.

https://flywaydb.org/documentation/migration/java

I am not sure how you would config Flyway to target a number of data sources via the its config files. My own development is based around using Java to call Flyway once per data source I need to work against. Spring Boot supports the autowiring of beans marked as @FlywayDataSource, but I have not looked into how this could be used.

For an in-java solution the code can be as simple as

    Flyway flyway = new Flyway();

    // Set the data source
    flyway.setDataSource(dataSource);

    // Where to search for classes to be executed or SQL scripts to be found
    flyway.setLocations("net.somewhere.flyway");

    flyway.setTarget(MigrationVersion.LATEST);
    flyway.migrate();