Although development of critical thinking skills has emerged as an important issue in undergraduate education, implementation of pedagogies targeting these skills across different science, technology, engineering, and mathematics disciplines has proved challenging. Our goal was to assess the impact of targeted interventions in 1) an introductory cell and molecular biology course, 2) an intermediate-level evolutionary ecology course, and 3) an upper-level biochemistry course. Each instructor used Web-based videos to flip some aspect of the course in order to implement active-learning exercises during class meetings. Activities included process-oriented guided-inquiry learning, model building, case studies, clicker-based think-pair-share strategies, and targeted critical thinking exercises. The proportion of time spent in active-learning activities relative to lecture varied among the courses, with increased active learning in intermediate/upper-level courses. Critical thinking was assessed via a pre/posttest design using the Critical Thinking Assessment Test. Students also assessed their own learning through a self-reported survey. Students in flipped courses exhibited gains in critical thinking, with the largest objective gains in intermediate and upper-level courses. Results from this study suggest that implementing active-learning strategies in the flipped classroom may benefit critical thinking and provide initial evidence suggesting that underrepresented and first-year students may experience a greater benefit.