Background Patient contact and clinical-based learning have been suggested as positive determinants of student motivation. However, few studies have been conducted on how this impacts dental student motivation. Based on the self-determination theory, this study aims to explore differences in the quality of motivation of dental student transition from preclinical (no previous patient contact) to clinical courses. Methods A longitudinal study was conducted with 95 Chilean students who completed the Academic Motivation Scale in two iterations over a one-year period. Results Paired t-test showed a significant increase in relative autonomous motivation as well as in amotivation. Discussions This suggests that while clinical contact supports student self-determination, an abrupt transition might be associated with maladjustment, which could lead to feelings of inadequacy and anxiety. Future research could usefully explore if early and gradual clinical experiences enhance student adaptation to the clinical context, thus increasing relative autonomous motivation and decreasing amotivation in the time.