Purpose Reduced bone mineral density of the distal femur (BMDDF) can persist long term after anterior cruciate ligament reconstruction (ACLR), even in athletes who return to high levels of competition. These deficits may have implications for the onset and progression of knee osteoarthritis. It is unknown if clinically modifiable factors are associated with losses in BMDDF. This study evaluated the potential influence of knee extensor peak torque (PT), rate of torque development (RTD), as well as peak knee flexion (PKF) angle and peak knee extensor moment (PKEM) during running, on longitudinal changes in BMDDF post-ACLR. Methods After ACLR, 57 Division I collegiate athletes underwent serial whole-body dual-energy x-ray absorptiometry (DXA) scans between 3 and 24 months post-ACLR. Of these, 43 athletes also had isometric knee extensor testing (21 female, 105 observations), and 54 had running analyses (26 female, 141 observations). Linear mixed-effects models, controlling for sex, assessed the influence of surgical limb quadriceps performance (PT and RTD), running mechanics (PKF and PKEM), and time post-ACLR on BMDDF (5% and 15% of femur length). Simple slope analyses were used to explore interactions. Results Athletes with RTD less than 7.20 (N·m)·kg−1·s−1 (mean) at 9.3 months post-ACLR demonstrated significant decreases in 15% BMDDF over time (P = 0.03). Athletes with PKEM during running less than 0.92 (N·m)·kg−1 (−1 SD below mean) at 9.8 months post-ACLR demonstrated significant decreases in 15% BMDDF over time (P = 0.02). Significant slopes were not detected at −1 SD below the mean for PT (1.75 (N·m)·kg−1, P = 0.07) and PKF (31.3°, P = 0.08). Conclusions Worse quadriceps RTD and running PKEM were associated with a greater loss of BMDDF between 3 and 24 months post-ACLR.