Overwhelming evidence demonstrating the benefits of active-learning pedagogy has led to a shift in teaching that requires students to interact more in the classroom. To date, few studies have assessed whether there are gender-specific differences in participation in active-learning science, technology, engineering, and mathematics (STEM) courses, and fewer have looked across different types of classroom participation. Over two semesters, we observed an introductory biology course at a large research-intensive university and categorized student participation into seven distinct categories to identify gender gaps in participation. Additionally, we collected student grades and administered a postcourse survey that gauged student scientific self-efficacy and salience of gender identity. We found that men participated more than expected based on the class composition in most participation categories. In particular, men were strongly overrepresented in voluntary responses after small-group discussions across both semesters. Women in the course reported lower scientific self-efficacy and greater salience of gender identity. Our results suggest that active learning in itself is not a panacea for STEM equity; rather, to maximize the benefits of active-learning pedagogy, instructors should make a concerted effort to use teaching strategies that are inclusive and encourage equitable participation by all students.