Background: Crohn's disease (CD) is a predisposing factor for bone loss and muscle dysfunction, which could lead to osteoporotic fractures and physical disability, respectively. Aim: To assess the effect of 6 months of combined impact and resistance training on bone mineral density (BMD) and muscle function in adults with CD. Methods: In this randomised controlled trial, 47 adults with stable CD were assigned to exercise (n = 23) or control (n = 24) groups and followed up for 6 months. The exercise group received usual care plus a 6-month combined impact and resistance training programme, involving three, 60-minute sessions per week and a gradual tapering of supervision to self-management. The control group received usual care alone. The primary outcomes were BMD (via dual energy X-ray absorptiometry) and muscle function (measures of upper and lower limb strength and endurance) at 6 months. Results: At 6 months, BMD values were superior in the exercise group with statistical significance at lumbar spine (adjusted mean difference 0.036 g/cm 2, 95% CI 0.024-0.048; P < 0.001), but not at femoral neck (0.018 g/cm 2, 0.001-0.035; P = 0.059) or greater trochanter (0.013 g/cm 2, −0.019 to 0.045; P = 0.415) after correcting for multiple outcomes. The exercise group also had superior values for all muscle function outcomes (P < 0.001; unadjusted mean differences ranging 22.6‒48.2%), and lower fatigue severity (P = 0.005). Three exercise-related adverse events were recorded: two instances of light-headedness and one of nausea. Conclusions: The intervention improved BMD and muscle function in adults with CD and appears as a suitable model of exercise for reducing future risk of osteoporotic fractures and disability. Trial registration: ISRCTN11470370.