Given the difficulty to perform exercise training wearing a mask, we examined differences in functional capacity improvement between masking during the coronavirus disease 2019 (COVID-19) pandemic and non-masking prior to the pandemic for patients undergoing cardiac rehabilitation (CR). Records of 660 patients who underwent and completed≥18 sessions of CR in 2018 (n=318, non-masking) and in 2022 (n=342, masking) at an academic health system were analyzed. The primary outcome was post-CR change in functional capacity in metabolic equivalents (MET) measured by exercise stress test. Sessions of CR participation and changes in depression, anxiety, and quality of life scores were secondary outcomes. We used multivariable linear regression to adjust for differences in baseline CR outcome measures, demographics, American Association of Cardiovascular and Pulmonary Rehabilitation (AACVPR) risk, and comorbid conditions. Baseline age (64.6±0.46yr), sex (28% female), and racial distribution (85% white) were similar between the masking and non-masking groups. Non-masking patients were more likely to be classified in the AACVPR high risk category and had lower anxiety scores at baseline compared to masking patients. After CR, both groups had similar and significant improvements in depression, anxiety, and quality of life scores, but the improvement in functional capacity was lower in the masking group (-0.62±0.12MET, P <.001) compared to the non-masking group. Results remained significant after multivariable adjustment. Cardiac rehabilitation patients requiring masking during the COVID-19 pandemic had less improvement in functional capacity than patients who did not wear masks during CR prior to the pandemic. Interventions to mitigate the potential side effects of masking for CR patients may require further exploration.