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Abstract Background During the COVID-19 pandemic, family physicians (FPs) served as the the initial point of contact for patients potentially infected with the virus, necessitating frequent updates to treatment protocols. However, practices also faced organizational challenges in providing care to other patients who also needed their medical attention. The pressure on FPs increased and affected their well-being. The international PRICOV-19 study, titled “Primary care in times of COVID-19 pandemic,” investigated how FPs functioned during the COVID‐19 pandemic. This article examines the correlation between various organizational and structural COVID-19-related variables and the well-being of FPs in Slovenia. Methods Between October 2020 and January 2021, we conducted an online cross-sectional survey. The questionnaire was distributed to 1040 Slovenian FPs and 218 family medicine (FM) trainees. Part of the questionnaire assessed the cooperation and well-being of FPs. The Mayo Clinic Well-being Index was used for the assessment. FP’s well-being was also assessed descriptively by asking open-ended questions about maintaining mental health during the pandemic. Potential factors associated with FPs’ well-being were identified using a multivariate linear regression method. Results The final sample comprised 191 participants (response rate 14.1%). The mean value ± standard deviation of the Mayo Well-being Index was 3.3 ± 2.6 points. The FPs with the poorest well-being had 5–15 years of work experience and worked in a practice where work could not be distributed in the absence of a co-worker without compromising the well-being of colleagues. Physical activity was identified as the most common method of maintaining mental health among FPs. Conclusions The results of the study suggest that targeted interventions are needed to support FPs mid-career, increase resilience in practice, promote strong team dynamics, and prioritise physical activity in healthcare. Addressing these aspects can contribute to the well-being of individual FPs and the overall health of the healthcare workers.