During the coronavirus disease 2019 (COVID-19) outbreak, family physicians (FPs) are the backbone of the healthcare system with considerable impact on the general population, and their well-being is of great importance. The aim of this investigation was to assess FPs mental health, as well as knowledge, attitudes and practices (KAPs) regarding the pandemic, and opinions on non-communicable disease (NCD) health care provided to patients. A cross-sectional study was carried out with a sample of 613 FPs. Anxiety and depression levels were estimated with the Hospital Anxiety and Depression Scale, subjective perceived stress with the Perceived Stress Scale, while trauma-related symptoms were assessed using the Impact on Event Scale-COVID19. KAPs toward the pandemic and opinions regarding NCD patients were evaluated with questionnaires accordingly. Results have shown that age (β = −0.02, p = 0.013) and personal risk of COVID‑19 (β = 1.05, p < 0.001) were significant independent correlates of the knowledge score. A total of 87.7% FPs expressed moderate/high perceived stress, 45.2% moderate/severe trauma-related symptoms, 60.4% borderline/abnormal anxiety levels, and 52.4% borderline/abnormal depression levels. Knowledge score was an independent predictor of perceived stress (β = −0.33, p = 0.023) and anxiety (β = −0.31, p = 0.006) levels. Limited accessibility to healthcare services and decreased number of newly-diagnosed NCD cases were mostly agreed on. The pandemic puts a considerable strain on FPs mental health, as well as on public health measures, due to the decreased overall quality of NCD patient health care. Educational programs may bridge the gaps between FPs’ knowledge. Thus lowering anxiety and improving patient care.