Background Evidence suggests that exercise training improves CVD risk factors. However, it is unclear whether health benefits are limited to aerobic training or if other exercise modalities such as resistance training or a combination are as effective or more effective in the overweight and obese. The aim of this study is to investigate whether 12 weeks of moderate-intensity aerobic, resistance, or combined exercise training would induce and sustain improvements in cardiovascular risk profile, weight and fat loss in overweight and obese adults compared to no exercise. Methods Twelve-week randomized parallel design examining the effects of different exercise regimes on fasting measures of lipids, glucose and insulin and changes in body weight, fat mass and dietary intake. Participants were randomized to either: Group 1 (Control, n?=?16); Group 2 (Aerobic, n?=?15); Group 3 (Resistance, n?=?16); Group 4 (Combination, n?=?17). Data was analysed using General Linear Model to assess the effects of the groups after adjusting for baseline values. Within-group data was analyzed with the paired t-test and between-group effects using post hoc comparisons. Results Significant improvements in body weight (-1.6%, p?=?0.044) for the Combination group compared to Control and Resistance groups and total body fat compared to Control (-4.4%, p?=?0.003) and Resistance (-3%, p?=?0.041). Significant improvements in body fat percentage (-2.6%, p?=?0.008), abdominal fat percentage (-2.8%, p?=?0.034) and cardio-respiratory fitness (13.3%, p?=?0.006) were seen in the Combination group compared to Control. Levels of ApoB48 were 32% lower in the Resistance group compared to Control (p?=?0.04). Conclusion A 12-week training program comprising of resistance or combination exercise, at moderate-intensity for 30 min, five days/week resulted in improvements in the cardiovascular risk profile in overweight and obese participants compared to no exercise. From our observations, combination exercise gave greater benefits for weight loss, fat loss and cardio-respiratory fitness than aerobic and resistance training modalities. Therefore, combination exercise training should be recommended for overweight and obese adults in National Physical Activity Guidelines.