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When using multiple databases, you probably won't be able to rely on autoconfiguration anymore, as Spring and Axon wouldn't know which one of the two databases you'd want to use.

Axon doesn't use an EntityManager directly. Instead, all components require an EntityManagerProvider. You may be able to use that to your advantage.

If you want all Axon components to use a certain database, simply define an EntityManagerProvider bean that returns the EntityManager that connects to that database. Spring manages the EntityManager completely, so you only need a single instance for all your EntityManager Sessions.

If you want different components to use different EntityManagers (e.g. Event Store in one database, Tokens and Sagas in another), then you will need to configure these components yourself. Sometimes, it's just easiest to copy the bean definitions from the AutoConfiguration classes and adapt them to suit your needs. See https://github.com/AxonFramework/AxonFramework/tree/master/spring-boot-autoconfigure/src/main/java/org/axonframework/springboot/autoconfig

Lastly, the entities that you need to scan depend on the components that you expect to use. Spring Boot autoconfiguration will scan the following Axon packages by default (if you don't specify any @EntityScan yourself):

• org.axonframework.eventhandling.tokenstore (for tokens)
• org.axonframework.modelling.saga.repository.jpa (for sagas)
• org.axonframework.eventsourcing.eventstore.jpa (for the event store)

Note that the @EnableJpaRepositories annotation is used to scan for @Repository classes. Axon doesn't use those, so there is no point scanning Axon packages for them. Axon does define entities, so @EntityScan will make sense.