Introduction: The COVID-19 pandemic has significantly changed the learning environment for medical students and affected their academic achievement. This study aims to determine the student’s clinical competency, learning environment, and its associated factors during the primary care medicine posting amid the COVID-19 pandemic. Methods: This is a cross-sectional study among medical students who had completed primary care medicine posting during the COVID-19 pandemic. Data on socio-demographic, posting characteristics, and students’ learning environment using the Dundee Ready Educational Environment Measure (DREEM) questionnaire and their objective structured clinical examination (OSCE) marks were collected. Independent t-test was used to compare DREEM scores between face-to-face and online groups. Multivariate analysis was used to determine factors associated with clinical competency and DREEM scores with p <0.05 considered significant. Results: A total of 205 students were recruited. Only 9.8% failed OSCE. Face-to-face teaching delivery (OR=3.61, 95 CI =1.03,11.30), face-to-face precept method (OR=1.24, 95 CI =1.12,12.51) and integrated curriculum (OR=5.23, 95 CI =1.03,26.47) were associated with good clinical competency. The total mean DREEM score was 72.94 (SD 28.8), with 89.3% having poor DREEM scores. Students who received face-to-face teaching scored higher in the Student’s Perceptions of Teacher domain compared to online teaching (p =0.036). Conclusion: Face-to-face teaching is preferred for good clinical competence and a learning environment. The impact of experiential learning was huge in our study, and it cannot be replaced by online learning. Furthermore, retraining teachers will improve the online learning experience for the students.