Process mining has grown into a mature research field with a wide range of techniques and applications. Much of this development builds on the pioneering work of Wil van der Aalst, whose contributions have shaped both the foundations and the growth of the discipline. Today, the field’s breadth raises the need for systematic methodological reflection to ensure that findings are robust and meaningful. In this paper, we provide a comprehensive discussion of threats to validity in process mining research. Building on the methodological framework of algorithm engineering, we analyze nine distinct validity concerns and examine how they apply across different streams of process mining. Our analysis highlights both established strengths and recurring challenges, drawing on examples from seminal contributions in the field, many inspired by Wil’s work.