Background: Digestive diseases have high incidence and mortality rates, posing a significant threat to global health. However, research on these disorders is uneven, while digestive cancers are well-studied and non-cancerous digestive diseases, despite their considerable health impact, have received less attention. Although cathepsins (CTSs), proteases that regulate extracellular matrix (ECM) turnover and cellular stiffness, have been implicated in digestive disorders, their role in disease-specific mechanical perturbations remains unclear. This study bridges this gap by integrating genetic causation with organ-level biomechanics. Methods: To overcome the constraints of conventional epidemiological methods, we employed a dual-sample bidirectional Mendelian randomization (MR) analysis leveraging genome-wide association study (GWAS) data to explore the causal relationships among 9 cathepsins and 23 non-cancerous digestive diseases. We conducted inverse variance weighted (IVW), weighted median (WM), MR-Egger, MR-PRESSO, Cochran’s Q, and sensitivity analyses for thorough evaluation. We also performed correlation analyses to link the biomechanical data with the genetic and disease outcomes, aiming to identify the relationships between mechanical factors, CTSs, and non-cancerous digestive diseases. Results: Forward MR analysis indicated that CTSB promotes both cholecystitis and cholelithiasis and CTSZ promotes chronic gastritis and diverticulosis. Higher CTSL2 levels promote non-alcoholic fatty liver disease (NAFLD) and liver cirrhosis, whereas upregulated CTSG reduces NAFLD risk. Reverse MR analyses indicated that gastroesophageal reflux, gastric ulcer, NAFLD, and cholecystitis elevated CTSE, G, Z, and B levels, respectively; non-alcoholic steatohepatitis elevates CTSB and H levels. Liver cirrhosis increases CTSB, S, and Z; Barrett’s esophagus, celiac disease, and diverticulosis downregulate CTSO, F, and H respectively; chronic pancreatitis lowers CTSE, F, and L2. Multivariable MR analyses revealed the independent effects of individual CTSs on specific diseases: CTSZ as a promoter for diverticulosis, CTSG as a protective factor for NAFLD, and CTSB as a promoter for cholecystitis and cholelithiasis. Conclusion: This study confirmed the causal relationships between cathepsins, mechanical factors in the digestive system, and non-cancerous digestive diseases. By integrating genetic and biomechanical analyses, we have provided a more in-depth understanding of how mechanical forces interact with biological molecules during the development of non-cancerous digestive diseases. Moreover, they may lead to the establishment of novel clinical practice approaches that take into account both the mechanical and biological aspects of digestive diseases, ultimately improving the diagnosis, treatment, and management of these conditions.