Although there is increasing evidence for a relationship between courses that emphasize student engagement and achievement of student deep learning, there is a paucity of quantitative comparative studies in a biochemistry and molecular biology context. Here, we present a pedagogical study in two contrasting parallel biochemistry introductory courses to compare student surface and deep learning. Surface and deep learning were measured quantitatively by a study process questionnaire at the start and end of the semester, and qualitatively by questionnaires and interviews with students. In the traditional lecture/examination based course, there was a dramatic shift to surface learning approaches through the semester. In the course that emphasized student engagement and adopted multiple forms of assessment, a preference for deep learning was sustained with only a small reduction through the semester. Such evidence for the benefits of implementing student engagement and more diverse non-examination based assessment has important implications for the design, delivery, and renewal of introductory courses in biochemistry and molecular biology.