The Biochemistry: Biomolecules Structure and Metabolism course's goal is to promote meaningful learning through an active learning environment. Thus, study periods (SP) and discussion groups (DG) are used as a substitute for lecture classes. The goal of this study was to evaluate how this learning environment influences students' motivation (n = 74). Motivation was evaluated by a questionnaire that was described in the literature and by comparing students' motivation in several courses. The results showed that the students had high achievement and low performance goals in this learning context. This indicates that students worked harder to learn than to get high grades. Students also had high self-efficacy, active learning strategies, and scientific learning values. Moreover, student's motivation in the active learning environment was higher than or equal to other courses in Pharmacy-Biochemistry. These results demonstrate that the active learning environment had a positive impact on students' motivation.