Configuration systems must be able to deal with inconsistencies which can occur in different contexts. Especially in interactive settings, where users specify requirements and a constraint solver has to identify solutions, inconsistencies may more often arise. In inconsistency situations, there is a need of diagnosis methods that support the identification of minimal sets of constraints that have to be adapted or deleted in order to restore consistency. A diagnosis algorithm’s performance can be evaluated in terms of time to find a diagnosis (runtime) and diagnosis quality. Runtime efficiency of diagnosis is especially crucial in real-time scenarios such as production scheduling, robot control, and communication networks. However, there is a trade off between diagnosis quality and the runtime efficiency of diagnostic reasoning. In this article, we deal with solving the quality-runtime performance trade off problem of direct diagnosis. In this context, we propose a novel learning approach based on matrix factorization for constraint ordering. We show that our approach improves runtime performance and diagnosis quality at the same time.