Metacognitive self-regulation is a crucial factor that promotes students' learning and achievement. However, the evidence regarding age differences in metacognitive skills is rather mixed, with some evidence pointing toward further refinement and development and other evidence suggesting declining levels. Academic motivation, an important antecedent of metacognitive self-regulation, has also been reported to decline steeply in adolescence. Hence, this raises the question whether there are any age-related differences in academic motivation and metacognitive self-regulation of adolescents and whether age differences in academic motivation drive decreases in metacognitive self-regulation. A large sample size of 1,027 Greek adolescents (ages 12-16, M age = 13.95, SD = 0.78) was utilized in the present study. Multigroup measurement invariance analyses were deployed to compare the latent means of motivational factors (self-efficacy, task value, mastery, and performance goals) and metacognitive self-regulation across age groups. Cholesky decomposition was applied to test the independent contribution of motivational factors to and the indirect effects of age on metacognitive self-regulation. Invariance analyses revealed scalar invariance for metacognitive self-regulation, language self-efficacy, mastery and performance goal orientations and partially scalar invariance for task value. Older adolescents scored lower on metacognitive self-regulation, mastery and performance goals, and self-efficacy. Older students scored lower on metacognitive self-regulation via indirect effects through Cholesky decomposed motivational factors. Self-efficacy, mastery and performance goals, and task value are similarly understood across adolescents in different age groups. Decreased mastery and performance goals and task value can lead to reduced metacognitive self-regulation in adolescents. The implications of the findings underscore the key role of making students more engaged with lessons' content in order to promote greater academic motivation and prevent decreases in metacognitive self-regulation.