Exercise training is advocated in insulin resistance and statins are used to treat hyperlipidaemia, two cardiometabolic risk factors often presenting concurrently. Statin intake may blunt mitochondrial function and the adaptive response to exercise training. Thus combining exercise training with statin administration may have adverse effects. We examined whether improvements in cardiometabolic risk factors, insulin sensitivity and mitochondrial function mediated by progressive exercise training are affected by statin use. A group of 14 obese elderly males on statins (ST) and 22 matched control subjects (C) were examined. Results on in vivo mitochondrial function [MRS (magnetic resonance spectroscopy)], mitochondrial density (Western blotting), insulin sensitivity (clamp) and metabolic flexibility (indirect calorimetry) were compared before and after a 12-week combined progressive exercise training programme (3×per week; 45 min per session). Except for LDL (low-density lipoprotein) cholesterol, all pre-training values were comparable between statin users and control subjects. In vivo mitochondrial function and mitochondrial density improved by training in both groups. Interestingly, blood-lipid profile, insulin sensitivity (+72%), non-oxidative and oxidative glucose disposal (+38% and +112%) and insulin-mediated suppression of fat oxidation (−62%) improved only in the ST group. We conclude that statin treatment did not impede exercise performance or tolerance, mitochondrial function or mass. In addition, training-induced improvements in glucose homoeostasis were preserved in the ST group. Strikingly, the insulin-sensitizing effect of training was more prominent in the ST group than in the C group. The combined prescription of statins along with exercise training is safe and should be considered for subjects prone to develop insulin resistance.