Anterior cruciate ligament (ACL) injuries are associated with significant loss of strength in knee extensor muscles that persists despite physical therapy. The underlying mechanisms responsible for this protracted muscle weakness are poorly understood; however, we recently showed significant myofiber atrophy and altered muscle phenotype following ACL injury. We sought to further explore perturbations in skeletal muscle morphology and progenitor cell activity following an ACL injury. Muscle biopsies were obtained from the injured and non-injured vastus lateralis of young adults (n = 10) following ACL injury, and histochemical/immunohistochemical analyses were undertaken to determine collagen content, abundance of connective tissue fibroblasts, fibrogenic/adipogenic progenitor (FAP) cells, satellite cells, in addition to indices of muscle fiber denervation and myonuclear apoptosis. The injured limb showed elevated collagen content (p < 0.05), in addition to a greater abundance of fibroblasts and FAPs (p < 0.05) in the injured limb. Fibroblast content was correlated with increased accumulation of extracellular matrix in the injured limb as well. A higher frequency of interstitial nuclei were positive for phospho-SMAD3 in the injured limb (p < 0.05), providing some evidence for activation of a fibrogenic program through transforming growth factor β following an ACL injury. The injured limb also displayed reduced satellite cell abundance, increased fiber denervation and DNA damage associated with apoptosis (p < 0.05), indicating alterations within the muscle itself after the ligament injury. Injury of the ACL induces a myriad of negative outcomes within knee extensor muscles, which likely compromise the restorative capacity and plasticity of skeletal muscle, impeding rehabilitative efforts. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1876-1885, 2017.