Following COVID-19, teaching was abruptly shifted from a live to a virtual format, posing a challenge to both students and faculty. There is a need to employ alternatives, emphasizing targeting the factors that suit Generation Z students for effective learning while maintaining social distancing. Understanding students' perceptions about the educational environment plays a vital role in planning and implementing teaching strategies for the future. Flipped teaching (FT) has been a successful instructional method because it embeds active learning strategies and some remote learning for which students are responsible. This study examined the perceptions of science, technology, engineering,and math (STEM) students (N = 265) while transitioning to online learning in classrooms implementing FT instruction for two cohorts: faculty expanding FT skills and novice FT faculty from a public university and a community college. Findings showed a significant difference between the two groups, with the transitions being more difficult in the courses taught by the novice versus the more experienced faculty (p < 0.01). Qualitative data analysis indicated that the FT classrooms eased the transition to fully online learning. The major challenges students faced were the lack of interaction with faculty and peers and a sense of community. In conclusion, FT eased the transition of college students in STEM courses to remote learning during COVID-19.