Background COVID-19 pandemic has affected all dimensions of day to day life across the world and medical education was no exception. With this study, we aimed to understand the effect of nationwide restrictions on medical education in Qatar, the models of education adopted during this period and perceptions of participants to the same. Methods We conducted a cross-sectional study utilizing an online questionnaire distributed via convenience sampling between April–October 2020. Study participants were faculty and trainees in governmental undergraduate and postgraduate medical education institutes. Two sets of questionnaires were designed for each group. They were asked a series of questions to assess pre- and post-COVID pandemic educational practices, their preferred teaching methods, and their familiarity with electronic teaching platforms. Faculty respondents were asked about their perceived barriers to delivery of medical education during the pandemic and their agreement on a 5-point Likert scale on specific elements. Trainees were asked a series of multiple-choice questions to characterize their pre- and post-COVID pandemic educational experiences. Both groups were asked open-ended questions to provide qualitative insights into their answers. Data were analysed using STATA software version 12.0. Results Majority of trainees (58.5%) responded that the pandemic has adversely affected medical education at both the undergraduate and postgraduate levels. Trainees (58.5%) and faculty (35.7%) reported an increased reliance on e-learning. Trainees preferred face-to-face education, while faculty preferred a combination of models of education delivery (33.5% versus 37.1%, p = 0.38). Although 52.5% of the faculty had no previous experience of delivering education through e-learning modalities, 58.9% however felt confident in using e-learning software. Conclusions Faculty and trainees agree that the COVID-19 pandemic has had a significant impact on the provision of medical education and training in Qatar, with an increased dependence on e-learning. As trainee’s prefer face-to-face models of education, we may have to consider restructuring of medical curricula in order to ensure that optimum learning is achieved via e-learning, while at the same time enhancing our use, knowledge and understanding of the e -learning methods. Further research is warranted to assess if these changes have influenced objective educational outcomes like graduation rates or board scores.