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Due to the COVID-19 pandemic, Canadian post-secondary educational programs, including Physical Therapy (PT), shifted to online instruction. This response resulted in curricular changes that emphasized theoretical learning due to the difficulties of teaching applied clinical skills online. This study used the Community of Inquiry framework to explore PT students’ perceptions of engagement in learning and developing clinical reasoning skills when PT programs shifted to online instruction in 2020. We conducted semi-structured interviews with 13 PT students from universities in a Canadian province. We identified three themes regarding participants’ perceptions of online learning during COVID-19 pandemic: instructors' role, engagement, and impact on knowledge application. Future studies may examine design considerations for online learning to address PT education requirements to support knowledge application.