Gender disparity in science, technology, engineering, and math (STEM) fields is an ongoing challenge. Gender bias is one of the possible mechanisms leading to such disparities and has been extensively studied. Previous work showed that there was a gender bias in how students perceived the competence of their peers in undergraduate biology courses. We examined whether there was a similar gender bias in a mechanical engineering course. We conducted the study in two offerings of the course, which used different instructional practices. We found no gender bias in peer perceptions of competence in either of the offerings. However, we did see that the offerings’ different instructional practices affected aspects of classroom climate, including: the number of peers who were perceived to be particularly knowledgeable, the richness of the associated network of connections between students, students’ familiarity with each other, and their perceptions about the course environment. These results suggest that negative bias against female students in peer perception is not universal, either across institutions or across STEM fields, and that instructional methods may have an impact on classroom climate. © 2019 Salehi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.