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Purpose We described patellofemoral alignment and trochlear morphology at one and five years after anterior cruciate ligament reconstruction (ACLR), and evaluated the associations between alignment and trochlear morphology (at one year) and worsening patellofemoral osteoarthritis (OA) features by five years. We also evaluated the associations between alignment and morphology to self-reported pain and function (Knee injury and Osteoarthritis Outcome Score, KOOS) at five years. Materials and methods In this longitudinal observational study, we followed 73 participants (mean age 29[9] years, 40% women) from one- to five-years after ACLR. Using MRI, we measured alignment and morphology, and scored cartilage and bone marrow lesions at both time points. We used mixed effects and linear regression models to achieve our stated aims. Results Greater lateral patella displacement increased risk of cartilage worsening (Odds Ratio [95% CI]: 1.09 [1.01, 1.16]); while less lateral tilt (0.91 [0.83, 0.99]) and greater trochlear angle (0.88 [0.77, 1.00]) were protective. Greater medial trochlear inclination increased risk of bone marrow lesion worsening (1.12 [1.04, 1.19]); while greater trochlear angle was protective (0.80 [0.67, 0.96]). Greater lateral displacement was associated with worse self-reported KOOS sport and recreation scores (β [95% CI]: −11.0 [−20.9, −1.2]) and quality of life scores (−10.5 [−20.4, −0.7]). Conclusions Lateral displacement, lateral tilt, and morphology at 1 year post-ACLR altered the risk of worsening patellofemoral OA features four years later. Lateral displacement was the only measure associated with worse self-reported symptoms at five years. These findings may lead to novel treatment strategies for secondary prevention after ACLR.