Set-theoretic methods and Qualitative Comparative Analysis (QCA) in particular are case-based methods. There are, however, only few guidelines on how to combine them with qualitative case studies. Contributing to the literature on multi-method research (MMR), we offer the first comprehensive elaboration of principles for the integration of QCA and case studies with a special focus on case selection. We show that QCA's reliance on set-relational causation in terms of necessity and sufficiency has important consequences for the choice of cases. Using real world data for both crisp-set and fuzzy-set QCA, we show what typical and deviant cases are in QCA-based MMR. In addition, we demonstrate how to select cases for comparative case studies aiming to discern causal mechanisms and address the puzzles behind deviant cases. Finally, we detail the implications of modifying the set-theoretic cross-case model in the light of case-study evidence. Following the principles developed in this article should increase the inferential leverage of set-theoretic MMR.