Recent research has indicated that autonomous motivation (e.g., pursuing a goal because it is enjoyable) is linked to greater preference for goal-congruent options (e.g., healthy food) and less of a preference for temptations (e.g., unhealthy food). Extending these findings, participants (n = 400) completed a mouse-tracking self-control paradigm where they were asked to choose between healthy and unhealthy foods (conflict condition) or healthy foods and inedible objects (comparison condition). Participants then completed a questionnaire about their goal to eat healthy, including their motivation.To assess goal conflict, we calculated each the area under the curve (AUC) for each trial, or the area between the idealized line from start to the healthy food and the participants' actual mouse trajectory. We hypothesized that area under the curve would be higher in the conflict trials and that autonomous motivation would be significantly associated with less goal conflict. Our hypotheses were supported as AUC was significantly higher in conflict trials, t(34,771) = -20.62, p < 0.001, and autonomous motivation was significantly associated with AUC, β = -0.001006, p < 0.001. Implications extend to further substantiating the link between motivation and goal conflict and establishing online mouse tracking studies as ecologically valid methodology.