Congenital patellar luxation (PL) and cranial cruciate ligament rupture (CCLR) are among the most prevalent hereditary musculoskeletal disorders in dogs. Despite their frequency, the microstructural alterations in the stifle joint capsule associated with these conditions remain poorly understood. This study aimed to characterize histomorphological changes in the joint capsule of dogs affected by PL and/or CCLR. Capsule samples were collected from dogs undergoing corrective surgery for PL or CCLR, while control tissue was obtained from dogs with unrelated orthopedic conditions. Histological evaluation assessed capsule thickness, the organization of its layers (stratum fibrosum, stratum subsynoviale, and stratum synoviale), synovial cell number, and villous or plicae formation. Associations with disease type, chronicity, sex, age, breed, and weight were analyzed. Dogs with PL and CCLR exhibited increased superficial synovial cell layers compared to controls, whereas chronic cases showed reduced villous formation (SEF = 2.46). Absence or marked reduction of the stratum subsynoviale correlated with PL and prolonged lameness. In PL cases, the stratum synoviale was frequently absent, whereas CCLR cases exhibited an increase in overall capsular thickness. These findings reveal distinct histomorphological remodeling in PL and CCLR, suggesting that chronic instability drives degenerative changes. Understanding these alterations may aid in early diagnosis, improve treatment strategies, and inform breeding programs targeting joint stability in predisposed breeds.