This paper explores the role and resolution of disagreements between physicians and their diagnostic AI-based decision support systems. With an ever-growing number of applications for these independently operating diagnostic tools, it becomes less and less clear what a physician ought to do in case their diagnosis is in faultless conflict with the results of the DSS. The consequences of such uncertainty can ultimately lead to effects detrimental to the intended purpose of such machines, e.g. by shifting the burden of proof towards a physician. Thus, we require normative clarity for integrating these machines without affecting established, trusted, and relied upon workflows. In reconstructing different causes of conflicts between physicians and their AI-based tools—inspired by the approach of “meaningful human control” over autonomous systems and the challenges to resolve them—we will delineate normative conditions for “meaningful disagreements”. These incorporate the potential of DSS to take on more tasks and outline how the moral responsibility of a physician can be preserved in an increasingly automated clinical work environment.