Achievement motivation theories propose that student motivation is composed of multiple factors. Models of self-regulated learning adopt this assumption and further articulate that multiple metacognitive processes--planning, monitoring learning, and self-evaluation--are essential to guide progress toward a learning goal. Learners' motivations are theorized to influence these metacognitive processes, which in turn influence learning outcomes. Latent profile analyses (LPA) enable a person-centered approach and capture multiple dimensions of motivation as they co-occur when learners engage in a task. This study documents the emergent motivation profiles of 1326 undergraduate biology students comprising efficacy beliefs, achievement goals, and perceptions of the value and costs of an anatomy and physiology course. Traces obtained from the learning management system provide data on students' use of tools designed to support metacognitive processes including planning, monitoring learning, and self-evaluation. Latent profiles document the emergence of motivation, and metacognition profiles and a 3-step process reveals how student demographics predict motivation profile membership, and how the motivation profiles are related to metacognition profiles. Four motivation profiles (High Cost, Moderately Motivated, High Goals and Values, Mastery-Driven) and 3 metacognitive learning profiles (Infrequent Metacognitive Processing; Planning and Self-Evaluation; Monitoring via Self-Assessment) emerged. Demographic information was found to predict motivation profile membership. Members of Mastery-Driven and High Cost groups were less likely to use tools that support metacognitive processing. Learners in High Goals and Values and Mastery-Driven groups outperformed those in other groups, and learners in Planning and Self-evaluation and Monitoring performance outperformed those with little metacognitive activity.