This study aims to shed light on animal management influences on the development of pathological changes observed on animal remains from the medieval site of Crkveno Brdo. Animal remains with abnormalities were discovered during archaeological excavations of the medieval settlement at the site of Crkveno Brdo in 2019. The site is situated near Senta in the northern region of modern‐day Serbia. The part of the settlement dated from the 11th to the 15th centuries was excavated. The percentage represented by various mammalian species documents that the most important economic species were cattle and horses, followed by sheep, goats, and pigs. Fishing and hunting were marginal in the settlement subsistence. The analyzed assemblage of bones with lesions consists of 39 specimens with 40 abnormalities. All of the remains exhibiting abnormalities were subjected to macroscopic and stereomicroscope analysis. The specimens with the most prominent changes also underwent x‐ray imaging and histopathological analysis. Almost all lesions were found in domestic animals. The most prevalent lesions in cattle, sheep, goat, and pig were dental and oral pathology, followed by articular abnormalities. In horses, 77% of pathological changes were articular abnormalities, and 11% dental and oral pathology, followed by traumatic lesions and inherited disorders (5.5% each). Congenital morphological variation is represented by a single specimen of horse lumbar vertebra. Pathological alterations were also noted in dogs, as was a severe healed tibiofibular fracture in a frog. Pathological alterations were related to external factors and specifically to patterns of animal management. Dental pathologies in cattle, sheep/goats, and pigs were primary attributed to malnutrition quality; articular abnormalities in horses, similar to aging and environmental factors, most likely work related.