Asymmetries are common during squats following anterior cruciate ligament reconstruction (ACLR). This study examined interlimb loading differences between squat phases at 6 months post-ACLR. Thirty-five participants performed bodyweight squats at self-selected speed and were analyzed using 3D motion capture. Vertical ground reaction force impulse (vGRFi), external knee flexion moment impulse (KFMi) and hip-to-knee flexion moment impulse ratio (HKRi) were calculated, along with interlimb ratios (ILR). Squat phase durations were also recorded. Paired t-tests and ANCOVA (controlling for time) were used to compare biomechanical variables across squat phases. Greater asymmetry was observed during ascent for vGRFi ILR (p = 0.045), KFMi ILR (p < 0.001) and HKRi ILR (p = 0.006). The ascent phase was faster than descent (p = 0.036). After adjusting for time, phase-related differences in ILRs were no longer significant. These findings suggest that greater limb and knee-specific loading asymmetries occur during the ascent phase of squats but may be influenced by movement speed. Importantly, significant knee-specific loading asymmetries persisted regardless of squat phase. At 6 months post-ACLR, addressing neuromuscular control and movement speed during rehabilitation may help reduce biomechanical imbalances during closed kinetic chain exercises.