Background The COVID-19 pandemic is affecting people in all nations worldwide. In Spain, the epidemic has become especially severe. The lack of protective measures is a major concern and may have caused emotional stress to Primary Care Physicians (PCPs). This study aimed to address the sources of psychological distress among Spanish PCPs during the COVID-19 pandemic.Methods This observational, cross sectional study was conducted using a survey questionnaire that consisted of 24 expressions to be answered by PCPs working in family healthcare centres in Spain during the pandemic. A specific scale, the “Examination of Anomalous Self-Experience”, EASE scale was used to determine the distress related to the care of COVID-19 patients among Spanish PCPs. A multivariate linear regression analysis was performed.Results In all, 518 PCPs belonging to different regions of Spain participated in this survey, of which 123 (23.7%) obtained high psychological distress scores. Only half of them had received information about the appropriate use of personal protective equipment (PPE). PCPs factors associated with higher levels of distress include female gender (1.69; CI 0.54, 2.84); Age (-0.43 (-0.61, 1.48)); working setting (rural) (0.84 (-0.34, 2.01)); lack of training in protective measures (1.96 (0.94, 2.99)). The absence of sick leave among colleagues, increased availability of PPEs, improved cleaning and hygiene conditions in health care centers facilities and the detection of COVID-19 RT-PCR for health care workers were associated with lower levels of distress.Conclusions One in four PCPs rated a high score for psychological distress. The availability of PPEs, training on their use, cleanliness and hygiene conditions in health care facilities and the availability of COVID-19 RT-PCR analyses for health workers, among others, are factors associated with the psychological distress of PCPs.