Aims It is evident that the COVID-19 pandemic has affected the medical practice and training of residents. In this study, we evaluated the physical examination (PE) habits of residents working in a university hospital and how their PE practices did change during the pandemic. Methods This single-centre, non-interventional, cross-sectional descriptive study was conducted in a university hospital using an online survey questionnaire between 5 and 20 October 2020. Results Of the 308 residents who participated in the study, 172 of them (55.8%) were female and the median age was 27 (IQR (3) = Q1 (29)-Q3 (26)). Amongst all, 263 participants (85.4%) declared that they have worked in the areas where suspected/confirmed COVID-19 patients were being served. A total of 262 (85%) residents stated that PE habits have changed generally during the pandemic. There was a significant difference with regards to the change in PE habits between those residents who have worked in the COVID-19 areas (n = 230, 87.5%) and those who have not (n = 32, 71.1%) (P = .004). PE habits of Internal Medicine Residents were changed more than others (P < .001). The main reason for the change in PE habits in general (77.9%) and during the examination of suspected/confirmed COVID-19 patients (89.7%) were "self-protection." Independent factors for limited PE in suspected/confirmed COVID-19 patients were found as "Avoiding performing physical examination to be exposed less/to protect (adjusted ORs = 13.067)," "relying on laboratory and radiological investigations during practice (adjusted ORs = 4.358)," and "not having a thought that reduced physical examination will render the diagnosis and course of COVID-19 (adjusted ORs = 2.244)." Conclusions This study clearly demonstrated that the COVID-19 pandemic has had a serious impact on the PE habits of the residents while examining patients in general and with COVID-19.