BackgroundThe Quintuple aim explicitly includes ‘health and wellbeing of the care team’ as requirement for the care of patients. Therefore, we examined working conditions, work engagement and health status of professionals active in primary care in Belgium (Flanders), and how these are interrelated.MethodsData of the cross-sectional ‘Health professionals survey of the Flemish Primary care academy’ of 2020 were examined. We performed logistic regression analyses to study the relationship between working conditions and self-reported dichotomized health of primary care professionals (sample size = 1033).ResultsThe majority of respondents (90%) reported having a good to very good general health and has a strong work engagement. Quality of employment was high, in particular regarding job security and supportive relations with colleagues, while less in terms of proper rewards and job career opportunities. Working as self-employee (vs. as salaried employee), and in a multidisciplinary group practice (vs. other organizational settings) were positively related to health. Work engagement and all dimensions of employment quality were related to general health, but work family balance, proper rewards, and perceived employability were independently positively related to self-reported health.ConclusionNine out of 10 Flemish primary care professionals working in diverse conditions, employment arrangements and organizational settings report good health. Work family balance, proper rewards, and perceived employability were important for primary care professionals’ health, and could provide opportunities to further strengthen the job quality and health of primary care professionals.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12875-023-02082-w.