The transition to online learning in spring 2020 was abrupt for both students and instructors. While many instructors moved to asynchronous classes, some institutions relied more heavily on synchronous online courses. Here, we evaluate student perceptions of an inquiry-based molecular biology lecture and lab course following this transition by comparing student survey responses from spring 2019, when the lecture and lab were fully in person, to spring 2020, when the lecture and lab started in person before transitioning to a synchronous online format. Students were asked to identify the main factors that supported their learning in lecture and lab, characterize the main barriers to learning in those courses, and discuss their preference of having an inquiry-based lab or a traditional "cookbook" lab with pre-determined answers. We coded these responses and provide one of the first studies to examine the impact of this online transition on student perceptions of learning in an inquiry-based molecular biology lecture and lab course.