Mouse-tracking is an increasingly popular method to trace cognitive processes. As is common for a novel method, the exact methodological procedures employed in an individual study are still relatively idiosyncratic and the effects of different methodological setups on mouse-tracking measures have not been explored so far. Here, we study the impact of one commonly occurring methodological variation, namely whether participants have to initiate their mouse movements to trigger stimulus presentation (dynamic starting condition) or whether the stimulus is presented automatically after a fixed delay and participants can freely decide when to initiate their movements (static starting condition). We compared data from a previous study in which participants performed a mouse-tracking version of a Simon task with a dynamic starting condition to data from a new study that employed a static starting condition in an otherwise identical setup. Results showed reliable Simon effects and Congruency Sequence effects on response time (RT) and discrete trial-level mouse-tracking measures (i.e., average deviation) in both starting conditions. In contrast, within-trial continuous measures (i.e., extracted temporal segments) were weaker and occurred in a more temporally compressed way in the static compared to the dynamic starting condition. This was in line with generally less consistent movements within and across participants in the static compared to the dynamic condition. Our results suggest that studies that use within-trial continuous measures to assess dynamic aspects of mouse movements should apply dynamic starting procedures to enhance the leakage of cognitive processing into the mouse movements.