Purpose To examine the relationship between tibiofemoral and patellofemoral joint articular cartilage and subchondral bone in the medial and gait biomechanics following partial medial meniscectomy. Methods For this cross-sectional study, 122 patients aged 30–55 years, without evidence of knee osteoarthritis at arthroscopic partial medial meniscectomy, underwent gait analysis and MRI on the operated knee once for each sub-cohort of 3 months, 2 years, or 4 years post-surgery. Cartilage volume, cartilage defects, and bone size were assessed from the MRI using validated methods. The 1st peak in the knee adduction moment, knee adduction moment impulse, 1st peak in the knee flexion moment, knee extension range of motion, and the heel strike transient from the vertical ground reaction force trace were identified from the gait data. Results Increased knee stance phase range of motion was associated with decreased patella cartilage volume (B = −17.9 (95 % CI −35.4, −0.4) p = 0.045) while knee adduction moment impulse was associated with increased medial tibial plateau area (B = 7.7 (95 % CI 0.9, 13.3) p = 0.025). A number of other variables approached significance. Conclusions Knee joint biomechanics exhibited by persons who had undergone arthroscopic partial meniscectomy gait may go some way to explaining the morphological degeneration observed at the patellofemoral and tibiofemoral compartments of the knee as patients progress from surgery.