Because you are not using configuration via XML, I believe you are using annotations. You own a class like this:
public class MongoConfig extends AbstractMongoConfiguration {...}
Thus, in addition to the annotations you should already have, add: @EnableMongoAuditing
Your configuration class will look like this now:
@Configuration
@EnableMongoRepositories(basePackages="...")
@EnableMongoAuditing
public class MongoConfig extends AbstractMongoConfiguration {...}
I hope this helps!