This study aimed to evaluate the risk of eating disorders, psychological distress, and health-related quality of life (HRQoL) in people with class 3 obesity (body mass index (BMI) ≥ 40 kg/m2), and the effect of multidisciplinary weight management over 12 months. This retrospective cohort study included all adults with class 3 obesity who enrolled in a weight management program from March 2018 to December 2019. Questionnaires included the Eating Disorder Examination Questionnaire Short (EDE-QS), Kessler Psychological Distress Scale (K10), and 36-Item Short Form Survey (SF-36) for HRQoL. Physical and Mental Component Summary scores (PCS and MCS) were derived from the SF-36. Of 169 participants who completed 12 months in the program, 65.7% (n = 111) completed questionnaires at baseline and 12 months, with 6.0 ± 6.8% weight loss over this period. Compared to baseline, there was significant improvement at 12 months in EDE-QS (15.7 ± 6.6 vs. 13.6 ± 6.2, p = 0.002), K10 (25.7 ± 9.7 vs. 21.2 ± 9.4, p < 0.001), PCS (29.4 ± 10.1 vs. 36.1 ± 10.9, p < 0.001), and MCS scores (40.2 ± 12.4 vs. 44.0 ± 13.4, p = 0.001). All, apart from EDE-QS scores, remained significant after adjusting for weight change. This study highlights the importance of multidisciplinary management in people with class 3 obesity to help reduce eating disorder risk and psychological distress, and improve HRQoL, in addition to weight loss.