Yes, handling associations between entities from different databases in Spring Boot with Spring Data JPA application is challenging, because JPA does not natively support cross-database relationships. We can solve this problem in two ways:

1. Handle the relationships manually:

As JPA does not support direct relationships between entities in separate databases:

• Store foreign keys manually instead of using @OneToOne or @OneToMany annotations.
• Retrieve related entities using service or repository layers instead of relying on JPA's built-in relationship mapping.

2. Use Database Links (if your database supports):

If your databases support the database links (such as DBLINK in Oracle or Federated Tables in MySQL), then you can:

• Create a view in one database that references the table from another.
• Treat that view as a regular entity in Spring Boot.

Since JPA does not support cross-database relationships, the best practice is to manage associations manually via service layers or use database links if your database supports them.