FarmCoSwiss is Switzerland's first agricultural cohort study on farmers’ health and wellbeing. It aims to longitudinally describe farmers’ mental and physical health and identify risk and protective factors. Between November 2022 and August 2023, the baseline survey assessed farm characteristics, lifestyle, occupational hazards, wellbeing, and physical and mental health. Descriptive statistics on selected variables were compared to the general population using Swiss Health Survey (SHS) data (2022) and the Swiss-wide SAPALDIA cohort (2020–2023). At baseline, 872 participants (65.9% men) were enrolled. Younger participants had better physical health-related quality of life (HRQoL), while older participants reported better mental HRQoL. Women had better physical, but worse mental HRQoL than men. Most participants (60.5%) had a BMI over 25. Compared to the Swiss general population, FarmCoSwiss participants sat less, consumed less alcohol and tobacco, but ate more red and processed meat. They reported lower prevalences of most diseases than SAPALDIA participants. Occupational accidents were common. Descriptive analyses indicate sex- and gender based differences in health challenges, highlighting the need for further research. Mental health issues, high rates of occupational accidents, and high BMI values call for in-depth studies. Given increasing political, societal, and environmental pressures on agriculture, these findings emphasize the importance of enhancing farmers’ health and wellbeing to maintain a thriving agricultural workforce.