The COVID-19 pandemic transformed the final year of undergraduate medical education for thousands of medical students across the globe. Out of concern for spreading SARS-CoV-2 and conserving personal protective equipment, many students experienced declines in bedside clinical exposures. The perceived competency of this class within the context of the pandemic is unclear. We designed and distributed a survey to measure the degree to which recent medical school graduates from the USA felt clinically prepared on 13 core clinical skills. Of the 1283 graduates who matched at HCA Healthcare facilities, 90% (1156) completed the survey. In this national survey, most participants felt they were competent in their clinical skills. However, approximately one out of four soon-to-be residents felt they were clinically below where they should be with regard to calling consultations, performing procedures, and performing pelvic and rectal exams. One in five felt they were below where they should be with regard to safely transitioning care. These perceived deficits in important skill sets suggest the need for evaluation and revised educational approaches in these areas, especially when traditional in-person practical skills teaching and practice are disrupted.