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Context: The COVID-19 pandemic has changed the structure of the healthcare system. As a response to the pandemic, the ministry of health applied many changes to the primary healthcare system. These changes created new challenges for healthcare workers (HCWs). Aims: To identify the roles and challenges of practitioners in primary healthcare (PHC) centers during COVID-19 in Al-Baha city, Saudi Arabia, in 2022. Methods and Materials: An analytical cross-sectional study was carried out in 2022 in Al-Baha city, Saudi Arabia. An electronic online questionnaire was distributed formally to HCWs in PHC centers. All primary HCWs during the COVID-19 pandemic in Al-Baha city, Saudi Arabia, were included. Results: A total of 424 responses were analyzed. Half (50.7%) of the participants had fieldwork roles during the pandemic. The two most commonly agreed-upon challenges were stress (78.7%) and worry about getting infected (79.8%). The majority (74.4%) of the participants’ roles involved direct contact with suspected COVID-19 cases, whereas 50.9% involved direct contact with confirmed COVID-19 cases. Direct contact with confirmed cases showed a significant association with worrying about getting infected (P = 0.019). Conclusions: Workload, overtime, conflict ambiguity, fear of getting and transmitting the infection, stress, and lack of personal protective equipment were challenges faced by the primary HCWs, which negatively impacted the quality of delivered services and mental health. We recommend facilitating access of primary HCWs to psychiatric clinics to improve stress and help cope with new roles during the pandemics and changes in the healthcare system.