XA support should be possible, but requires additional metadata (at least the datasource class name) a different set of code generations and supporting logic. The built-in xa support for spring (spring.datasource.xa) seems to only account for only a single source. Atomikos has support for mulitple XA: http://www.thedevpiece.com/configuring-multiple-datasources-using-springboot-and-atomikos/

Perhaps narayana could add something similar so that there is a simple properties driven bean that can be created for each datasource.