Purpose To examine articular cartilage and subchondral bone changes in tibiofemoral and patellofemoral joints following partial medial meniscectomy. Methods For this cross-sectional study, 158 patients aged 30-55 years, without evidence of knee osteoarthritis at arthroscopic partial medial meniscectomy (APMM), and 38 controls were recruited. MRI was performed once on the operated knee for each subcohort of 3 months, 2 or 4 years post-surgery, and the randomly assigned knee of the controls. Cartilage volume, cartilage defects, and bone size were assessed using validated methods. Results Compared with controls, APMM patients had more prevalent cartilage defects in medial tibiofemoral (OR = 3.17, 95%CI 1.24-8.11) and patellofemoral (OR = 13.76, 95%CI 1.52-124.80) compartments, and increased medial tibial plateau bone area (B = 143.8, 95%CI 57.4-230.2). Time from APMM was positively associated with cartilage defect prevalence in medial tibiofemoral (OR = 1.02, 95%CI 1.00-1.03) and patellofemoral (OR = 1.04, 95%CI 1.01-1.07) compartments, and medial tibial plateau area (B = 2.5, 95%CI 0.8-4.3), but negatively associated with lateral tibial cartilage volume (B = -4.9, 95%CI -8.4 to -1.5). The association of APMM and time from APMM with patellar cartilage defects was independent of tibial cartilage volume. Conclusions Partial medial meniscectomy is associated with adverse effects on articular cartilage and subchondral bone, which are associated with subsequent osteoarthritis, in both tibiofemoral and patellofemoral compartments. Level of evidence III.