Learning assistant (LA) programs have been implemented at a range of institutions, usually as part of a comprehensive curricular transformation accompanied by a pedagogical switch to active learning. While this shift in pedagogy has led to increased student learning gains, the positive effect of LAs has not yet been distinguished from that of active learning. To determine the effect that LAs would have beyond a student-centered instructional modality that integrated active learning, we introduced an LA program into a large-enrollment introductory molecular biology course that had already undergone a pedagogical transformation to a highly structured, flipped (HSF) format. We used questions from a concept test (CT) and exams to compare student performance in LA-supported HSF courses with student performance in courses without LAs. Students in the LA-supported course did perform better on exam questions common to both HSF course modalities but not on the CT. In particular, LA-supported students' scores were higher on common exam questions requiring higher-order cognitive skills, which LAs were trained to foster. Additionally, underrepresented minority (URM) students particularly benefited from LA implementation. These findings suggest that LAs may provide additional learning benefits to students beyond the use of active learning, especially for URM students.