To determine the cross-sectional and longitudinal associations of patella alignment with cartilage relaxation and patients' self-reported symptoms. Thirty participants with isolated patellofemoral joint (PFJ) degeneration (six males, 53.7 ± 9.3 years) and 24 controls (12 males, 47.6 ± 10.7 years) were included. Magnetic resonance assessment was performed to provide grading of structural abnormalities, cartilage relaxation times, and patella alignment. Self-reported symptoms were assessed using the self-administrated knee injury and osteoarthritis outcome score (KOOS). All participants were examined at baseline and 3 years. Statistical parametric mapping and Pearson partial correlation were used to evaluate the associations between patella alignment with cartilage relaxation times and self-reported symptoms, respectively. The analyses were performed between baseline (cross-sectional) as well as the baseline against 3 years (longitudinal). Results indicated that patella height and patella flexion were associated with T_1ρ and T₂ relaxation times at baseline (percentages of voxels showing significant correlation [PSV] = 10.1%–24.8%;​ mean correlations [R] = 0.34–0.36;​ mean p = 0.015–0.026). Furthermore, greater patella lateral alignment, lateral tilt, and lateral spin were associated with longer T2 times at 3 years (PSV = 11.0%–14.4%, R = 0.39–0.44, p = 0.017–0.028). Last, a higher patella was associated with a lower KOOS at baseline and at 3 years (R = −0.33 to −0.35). The study suggests that patella malalignment is a risk factor for worsening cartilage health, informing clinicians of a better rehabilitation program that targets PFJ degeneration.