Background: Anterior cruciate ligament (ACL) injuries may lead to long-term neuromuscular and structural adaptations in thigh muscles. Although quadriceps dysfunction is well reported, chronic changes in other muscle groups, especially in nonoperatively managed ACL-deficient individuals, remain poorly understood. Methods: The present cohort study utilized Osteoarthritis Initiative data to assess longitudinal thigh muscle changes in individuals with ACL tears confirmed on magnetic resonance imaging (MRI) and no history of reconstruction. A validated deep-learning model segmented muscle cross-sectional area and quantified intra-muscular adipose tissue and contractile percentage. Quantitative MRI data were obtained at baseline and at 4-year follow-up. Propensity score matching (1:2 to 1:3) controlled for baseline covariates. Strength was assessed with use of standardized Osteoarthritis Initiative protocols. Linear mixed-effects models compared longitudinal changes between ACL-deficient and ACL-intact thighs. Results: A total of 1,207 thighs were analyzed, including 92 with ACL tears and 1,115 controls, with a mean patient age of 61 ± 9 years. Over 4 years, ACL-deficient thighs exhibited progressive hamstring atrophy (−28.18 mm 2 /year; 95% confidence interval, −42.43 to −13.92; p < 0.001) and sartorius atrophy (−3.02 mm 2 /year; 95% confidence interval, −5.15 to −0.89; p = 0.006). No significant differences were observed in quadriceps or adductor cross-sectional area. Hamstring force decreased significantly (−3.49 N/year; 95% confidence interval, −6.62 to −0.36; p = 0.029), whereas quadriceps force and specific force showed no significant changes. Intra-muscular adipose tissue and contractile percentage did not significantly differ between groups. Findings had been similar in unmatched patients Conclusions: The present findings highlight selective muscle deterioration in the posterior thigh muscles following ACL injury, with minimal changes in quadriceps morphology, over time. These results underscore the importance of long-term, targeted rehabilitation strategies focusing on hamstring preservation. This study represents the first longitudinal matched-cohort analysis of muscle morphology and fat infiltration in unreconstructed ACL-deficient knees. Level of Evidence: Prognostic Level II . See Instructions for Authors for a complete description of levels of evidence.