Exercise is Medicine Canada (EIMC) is an initiative that promotes physical activity (PA) counselling and exercise prescription within health care. The purpose of this study was to compare physicians' perceptions and practices around PA counselling and exercise prescription following EIMC training. Physicians (n = 46) from 7 different provinces completed questionnaires initially and 3 months following an EIMC workshop. Three months after intervention, physicians reported greater confidence compared with baseline for providing physical activity and exercise (PAE) information to patients (79% vs 55%; p < 0.001), assessing patients' PAE (69% vs 44%, p = 0.005), answering patients' PAE questions (78% vs 54%, p < 0.001), providing PAE advice (71% vs 43%, p < 0.001), and identifying which patients would benefit from referral to qualified exercise professionals (77% vs 52%, p = 0.002). At follow-up, physicians reported PA prescription barriers as less impactful (out of 4; all p < 0.05), including perceived patients' lack of interest (2.75 to 2.25), lack of available resources (2.59 to 2.00), and lack of time (2.41 to 2.14). The proportion of physicians providing written exercise prescriptions increased from 20% to 74%. This study suggests that the completion of a 1-day EIMC workshop increases physicians' confidence, knowledge, and counselling behaviours of physicians in prescribing PAE.