ACL tears are a common type of injury that often happens during sports activities. While some people may regain knee function after healing, the development of post-traumatic osteoarthritis (PTOA) is a possible long-term outcome of a knee injury. The integrity of many tissues is affected by the injury including bone, which typically experiences density loss. Subregional analysis of bone density using medical imaging provides more detailed insight into bone status after an acute knee injury, however these spatial positions may overlook areas with significant local change. This work examined patterns of bone change through the distal femur and proximal tibia following an ACL tear using computed tomography (CT) images of 10 participants. Clinical CT and high resolution peripheral quantitative CT (HR-pQCT) scans of injured knees were measured at baseline and 1-year follow-up time points. The longitudinal data were registered, and the voxel-wise differences were visualized to identify regions of significant bone changes and compare the two modalities. Patterns of bone density changes were assessed in the context of individual patient locations of bone contusions, fractures, and osteochondral injuries, as described in baseline magnetic resonance imaging (MRI) reports. In the femur, bone loss was observed at both condyles and, for 90% of participants, bone loss was also observed at the site of insertion of the ACL. Posterior horn meniscus injury typically corresponded to bone loss on the associated femoral condyle, and on the posterior tibial plateau. Widespread changes to bone density in the injured knee are influenced not only by ACL tear, but by concurrent injuries such as meniscal damage. These significant changes within the first year post injury may play an important role in the long term health of the knee.