Abstract: Query answering over inconsistent knowledge bases is a problem that has attracted a great deal of interest over the years. Different inconsistency-tolerant semantics have been proposed, and most of them are based on the notion of repair, that is, a "maximal" consistent subset of the database. In general, there can be several repairs, so it is often natural and desirable to express preferences among them. In this paper, we propose a framework for querying inconsistent knowledge bases under user preferences for existential rule languages. We provide generalizations of popular inconsistency-tolerant semantics taking preferences into account and study the data and combined complexity of different relevant problems.