Doctoral students' well-being and motivation are important factors that are both shaped by, and shape students' academic experiences in their programs. Existing literature consistently highlights the concerning well-being and maladaptive motivational patterns in doctoral students, but no research to date attempted to explore some of the structural features associated with these wellness and achievement factors in a large-scale study. The present study examined whether doctoral program phase (i.e. coursework, comprehensive examination, or dissertation phase had an effect on 3004 doctoral students' well-being levels (stress, depression, program satisfaction, and illness symptoms) and motivation (self-determined motivation and self-efficacy). Results revealed doctoral students to report the highest well-being and internal motivation during the coursework phase, while the comprehensive examination phase was found to be the most challenging for most students as indicated by the lowest wellness and motivation scores. A discussion of the present results and their theoretical and practical implications ensues.