This study investigated daily motivation regulation as a multilevel mediator of undergraduate students’ intrinsic and extrinsic motivation and academic functioning. Undergraduate students (N = 124) completed measures on motivation, motivation regulation, and study time for 10 consecutive days leading up to a statistics exam. Bayesian multilevel mediation models were used to examine motivation regulation as a mediator between motivation and daily study time at the within-person level and exam performance at the between-person level. Within-person findings revealed motivation regulation mediated the relation between both intrinsic and extrinsic motivation and study time although the indirect effect was substantially stronger for extrinsic motivation. Between-person findings did not support mediation between intrinsic and extrinsic motivation and exam performance. Specifically, none of the motivation or motivation regulation factors predicted students’ exam performance. It appears that motivation regulation typically stems from extrinsic motivation and is more closely associated with process-oriented rather than product-oriented academic functioning.