Abstract Background The COVID-19 pandemic markedly changed how healthcare services are delivered and telehealth delivery has increased worldwide. Whether changes in healthcare delivery borne from the COVID-19 pandemic impact effectiveness is unknown. Therefore, we examined the effectiveness of exercise physiology services provided during the COVID-19 pandemic. Methods This prospective cohort study included 138 clients who received exercise physiology services during the initial COVID-19 pandemic. Outcome measures of interest were EQ-5D-5L, EQ-VAS, patient-specific functional scale, numeric pain rating scale and goal attainment scaling. Results Most (59%, n = 82) clients received in-person delivery only, whereas 8% (n = 11) received telehealth delivery only and 33% (n = 45) received a combination of delivery modes. Mean (SD) treatment duration was 11 (7) weeks and included 12 (6) sessions lasting 48 (9) minutes. The majority (73%, n = 101) of clients completed > 80% of exercise sessions. Exercise physiology improved mobility by 14% (β = 0.23, P = 0.003), capacity to complete usual activities by 18% (β = 0.29, P < 0.001), capacity to complete important activities that the client was unable to do or having difficulty performing by 54% (β = 2.46, P < 0.001), current pain intensity by 16% (β = − 0.55, P = 0.038) and goal attainment scaling t-scores by 50% (β = 18.37, P < 0.001). Effectiveness did not differ between delivery modes (all: P > 0.087). Conclusions Exercise physiology services provided during the COVID-19 pandemic improved a range of client-reported outcomes regardless of delivery mode. Further exploration of cost-effectiveness is warranted.