Background Clinical competency is the ability to integrate knowledge, skills, attitudes and values into a clinical situation and it is very important in nursing education, clinical settings, nursing management, and crises. This study aimed to investigate nurses’ professional competence and its correlates before and during the COVID-19 pandemic. Methods We conducted this cross-sectional study before and during the COVID-19 outbreak and recruited all nurses working in hospitals affiliated to Rafsanjan University of Medical Sciences, southern Iran, so we included 260 and 246 nurses in the study before and during the COVID-19 epidemic, respectively. Competency Inventory for Registered Nurses (CIRN) was used to collect data. After inputting the data into SPSS24, we analysed them using descriptive statistics, chi-square and multivariate logistic tests. A significant level of 0.05 was considered. Results The mean clinical competency scores of nurses were 156.97 ± 31.40 and 161.97 ± 31.36 before and during the COVID-19 epidemic, respectively. The total clinical competency score before the COVID-19 epidemic was not significantly different from that during the COVID-19 epidemic. Interpersonal relationships (p = 0.03) and desire for research/critical thinking (p = 0.01) were significantly lower before the COVID-19 outbreak than during the COVID-19 outbreak. Only shift type had an association with clinical competency before the COVID-19 outbreak, while work experience had an association with clinical competency during the COVID-19 epidemic. Conclusion The clinical competency among nurses was moderate before and during the COVID-19 epidemic. Paying attention to the clinical competence of nurses can improve the care conditions of patients, and nursing managers should improve the clinical competence of nurses in different situations and crises. Therefore, we suggest further studies identifying factors improving the professional competency among nurses.