Multiple Transaction Managers in Spring Boot for different EntityManagers

See if this works:

@Bean
@Primary
@ConfigurationProperties(prefix = "datasource.admin")
public DataSource adminDS() { ... }

@Bean
@Primary
public LocalContainerEntityManagerFactoryBean adminEMF(...) { ... }

@Bean
@Primary
public JpaTransactionManager adminTM(...) { ... }

@Bean
public LocalContainerEntityManagerFactoryBean appEMF(...) { ... }

@Bean
public JpaTransactionManager appTM(...) { ... }

The only change I have made from your configuration is to declare a transaction manager for the admin side explicitly and marked that transaction manager as the default.