Students' motivation plays an important role in successful science learning. However, motivation is a complex construct. Theories of motivation suggests that students' motivation must be conceptualized as a motivational system with numerous components that interact in complex ways and influence metacognitive processes such as self-evaluation. This complexity is further increased because students' motivation and success in science learning influence each other as they develop over time. It is challenging to study the co-development of motivation and learning due to these complex interactions which can vary widely across individuals. Recently, person-centered approaches that capture students' motivational profiles, that is, the multiplicity of motivational factors as they co-occur in students, have been successfully used in educational psychology to better understand the complex interplay between the co-development of students' motivation and learning. We employed a person-centered approach to study how the motivational profiles, constructed from goal-orientation, self-efficacy, and engagement data of N = 401 middle school students developed over the course of a 10-week energy unit and how that development was related to students' learning. We identified four characteristic motivational profiles with varying temporal stability and found that students' learning over the course of the unit was best characterized by considering the type of students' motivational profiles and the transitions that occurred between them. We discuss implications for the design and implementation of interventions and future research into the complex interplay between motivation and learning.