Due to COVID-19, universities across Canada were forced to undergo a transition from classroom-based face-to-face learning and invigilated assessments to online-based learning and non-invigilated assessments. This study attempts to empirically measure the impacts of COVID-19 on students’ marks from eleven science, technology, engineering, and mathematics (STEM) courses using a Bayesian linear mixed effects model fitted to longitudinal data. The Bayesian linear mixed effects model is designed for this application which allows student-specific error variances to vary. The novel Bayesian missing value imputation method is flexible which seamlessly generates missing values given complete data. We observed an increase in overall average marks for the courses requiring lower-level cognitive skills according to Bloom's Taxonomy and a decrease in marks for the courses requiring higher-level cognitive skills, where larger changes in marks were observed for the underachieving students. About half of the disengaged students who did not participate in any course assessments after the transition to online delivery were in special support.