Laboratory sessions are designed to develop the experimental skills and the acquaintance with instruments that may contribute to a successful career in Biochemistry and associated fields. This study is a report on improving a traditional Biochemistry course by devising the laboratory sessions as an inquiry-based environment to develop the students' autonomy to plan, perform, and interpret experiments. We reformulated our Biochemistry laboratory to have three activities that sequentially increase regarding autonomy. We used an autonomy support structure consisting of varying levels of engagement by the student in such aspects as Organizational, Procedural, and Cognitive, gradually transferring to students the responsibility for their decisions within the laboratory. Our results show that students performed better on the less instructed worksheet activities, characterized by a more complex autonomy support, as compared to the activities tightly controlled by worksheet directions. A review of the group lab reports suggests that students showed skills required to work with different levels of autonomy. Thus, this approach has positively supported the students' autonomy, not only mapping their progress through the activities proposed but also encouraging them to make decisions during their experiments and stimulating their ability to think and to plan experiments themselves.