The objective of this randomized controlled trial was to investigate the effect of adding either aerobic training (AT) or resistance training (RT) to a multidisciplinary teamed (MDT) educational weight management programme on the health-related fitness of morbidly obese individuals. Males (n = 9) and females (n = 24) aged between 24 and 68 years with a body mass index (BMI) of ≥40 kg m2 (≥35 kg m2 with comorbidities) undertaking a weight management programme were recruited (Completion: M = 8, F = 19). Participants were randomly allocated to either AT (n = 12), RT (n = 11) or CON (n = 10). AT and RT undertook three structured ∼60 min moderate intensity sessions weekly, two supervised gym-based and one structured home-based session for 12 weeks; CON undertook usual care alone. Anthropometric, psychological and functional capacity measures were obtained pre- and post-intervention. Both exercise interventions elicited improvements compared with CON in the: shuttle walk test (AT [Δ 207.0 ± 123.0 metres, 68.0%, P = 0.04], RT [Δ 165.0 ± 183.3 m, 48.8%, P = 0.06], CON [Δ −14.3 ± 38.7 m, −6.2%]), triceps skin-fold (P ≤ 0.001), self-efficacy (P = 0.005) and interest/enjoyment (P = 0.006). RT displayed additional improvements compared with CON in BMI (RT [Δ −1.02 ± 0.91 kg·m2, −2.5%, P = 0.033], AT [Δ −1.84 ± 2.70 kg·m2, −4.3%, P = 0.142], CON [Δ −0.31 ± 1.47 kg·m2, −0.6%]), waist circumference (P = 0.022), competence (P = 0.019), biceps skin-fold (P = 0.012) and medial calf skin-fold (P = 0.013). No significant differences were observed between exercise modalities. Regardless of exercise mode, the addition of supervised and structured exercise to a MDT weight management programme significantly improved anthropometric, functional and psychological measures in obese participants with a BMI of ≥35 kg·m2.