Hybrid classrooms (taught simultaneously to both in-person and online students) have become increasingly common in the course of the coronavirus disease 2019 (COVID-19) pandemic, and they have offered multiple benefits and challenges. We offer several recommendations to improve student engagement and classroom experience in such classrooms, especially for online learners who may face greater barriers to participation. These recommendations were constructed based on survey responses from students in a microbiology classroom who were categorized as in-person or online learners depending on their chosen modalities. Briefly, increasing familiarity, encouraging but not mandating camera use in online small groups, tailoring active learning activities for the online population, and enabling access to lecture recordings and transcripts were identified as strategies that would promote student engagement and improve student outcomes. As online learning will likely play an important role in higher education in the future, educators will need to continue to rethink and adapt some familiar classroom strategies to resonate with a virtual audience. In any case, lessons learned in a hybrid course can be applied to a range of teaching modalities, to provide students with a more engaging and supportive learning environment.