Mouse-tracking is an increasingly popular process-tracing method. It builds on the assumption that the continuity of cognitive processing leaks into the continuity of mouse movements. Because this assumption is the prerequisite for meaningful reverse inference, it is an important question whether the assumed interaction between continuous processing and movement might be influenced by the methodological setup of the measurement. Here we studied the impacts of three commonly occurring methodological variations on the quality of mouse-tracking measures, and hence, on the reported cognitive effects. We used a mouse-tracking version of a classical intertemporal choice task that had previously been used to examine the dynamics of temporal discounting and the date–delay effect (Dshemuchadse, Scherbaum, & Goschke, 2013). The data from this previous study also served as a benchmark condition in our experimental design. Between studies, we varied the starting procedure. Within the new study, we varied the response procedure and the stimulus position. The starting procedure had the strongest influence on common mouse-tracking measures, and therefore on the cognitive effects. The effects of the response procedure and the stimulus position were weaker and less pronounced. The results suggest that the methodological setup crucially influences the interaction between continuous processing and mouse movement. We conclude that the methodological setup is of high importance for the validity of mouse-tracking as a process-tracing method. Finally, we discuss the need for standardized mouse-tracking setups, for which we provide recommendations, and present two promising lines of research toward obtaining an evidence-based gold standard of mouse-tracking.