During the global COVID-19 pandemic, instructors strove to facilitate student learning, engagement, and community in an unfamiliar environment, while students adapted to a college experience that differed from their expectations. This context provided the opportunity to identify factors that increased undergraduates’ sense of belonging in remote STEM classrooms. We analyzed responses from 1589 students in 26 undergraduate STEM courses at a large R1 research university in Likert-style surveys to assess how the remote modality affected their sense of belonging in their STEM course. Likewise, we analyzed data from 22 instructors about their pedagogical mindset and implementation of classroom activities. K-means clustering of student survey responses sorted classes into four significantly distinct clusters. Student responses in cluster 1 revealed an increased sense of belonging in the post-survey, whereas students in cluster 4 reported a decreased sense of belonging. Further, we observed that a higher frequency of active learning activities (student–student and student-instructor interactions) and instructor type (teaching faculty) correlated with an increased sense of belonging. Many studies have investigated alterations in students’ sense of belonging; our study contributes by identifying activities that enhance a sense of belonging in remote STEM classrooms. Moreover, our findings from a quantitative study allow us to propose ways instructors can modify their courses to increase student sense of belonging and insulate students from the isolation of remote classrooms.