Objective: To examine the effects of a 16-week exercise programme, using either a hybrid cycle or a handcycle, on cardiovascular disease risk factors in people with spinal cord injury. Participants: Nineteen individuals with spinal cord injury ≥ 8 years. Design: Multicentre randomized controlled trial. Both the hybrid cycle group (n = 9) and the handcycle group (n = 10) trained twice a week for 16 weeks on the specific cycle. Outcome measures obtained pre and post the programme were: metabolic syndrome components (waist circumference, systolic and diastolic blood pressure, high-density lipoprotein cholesterol, triglycerides and insulin resistance), inflammatory status (C-reactive protein (CRP), interleukin (IL)-6 and -10), and visceral adiposity (trunk and android fat). Results: For all outcome measures, there were no significant differences over time between the 2 training groups. Overall significant reductions were found for waist circumference (p = 0.001), diastolic blood pressure (p = 0.03), insulin resistance (p = 0.006), CRP (p = 0.05), IL-6 (p = 0.04), IL-6/IL-10 ratio (p = 0.03), and trunk (p = 0.04) and android (p = 0.02) fat percentage. No significant main effects for time were observed for systolic blood pressure, triglycerides, high-density lipoprotein cholesterol, IL-10, and trunk and android fat mass. Conclusion: The 16-week exercise programme, using either a hybrid cycle or a handcycle, found similar beneficial effects on metabolic syndrome components, inflammatory status and visceral adiposity, indicating that there were no additional benefits of functional electrical stimulation-induced leg exercise over handcycle exercise alone.