Aim: This study examines the impact of different fertiliser types – phosphate, nitrogen, and potash –and pesticide use on disability-adjusted life years (DALYs) associated with digestive system diseases in European countries. It focuses on pancreatitis, upper digestive system disorders, and non-alcoholic fatty liver disease (NAFLD), including cirrhosis. Materials and Methods: Using a balanced panel dataset covering 39 European countries from 2006 to 2021, the study incorporates data from the Global Burden of Disease database (DALYs), the Food and Agriculture Organization (fertiliser and pesticide use), and the World Bank (trade indicators). A fixed-effect regression model was applied to assess the influence of agricultural chemical use and trade dynamics on DALYs. Results: Pesticide use per hectare was significantly associated with higher DALYs for NAFLD, indicating substantial health risks. Nitrogen fertiliser use showed a protective effect against DALYs for upper digestive diseases and pancreatitis. In contrast, excessive potash application was linked to increased DALYs for pancreatitis. The effects of phosphate use varied by disease type. Trade-related interaction terms demonstrated complex and sometimes amplifying effect on health outcomes. Conclusions: Agricultural inputs have both beneficial and adverse health implications. While essential for productivity, their misuse can contribute to chronic disease burdens. The findings highlight the importance of sustainable farming practices and regulatory oversight. Integrating health metrics such as DALYs into agricultural and environmental policy could improve public health outcomes across Europe.