The association of a well-balanced diet with exercise is a key strategy to treat obesity. Whereas exercise is known to induce beneficial effects on bone, data concerning these effects in a weight loss program in rat are lacking. Because weight loss is linked to a concomitant bone loss, we wondered if exercise training duration may differently affect the bone tissue in such a program. This study aimed to investigate bone responses to two different durations of exercise training combined with a well-balance diet in obese rats. Fifty nine Wistar male rats were previously fed with a high fat/high sucrose diet (HF/HS) for 4 months to induce obesity. A control group (n = 15) was fed with a standard diet (HF/HS vs. Control = T0). Then, all rats were given a well-balanced diet and assigned to 4 different modalities: one month of exercise training (treadmill: 50 min/day, 5 days/week) or sedentarity (T1), two months of exercise or sedentarity (T2). The body composition and BMD were assessed by DXA. Visceral fat mass was weighed and insulin sensitivity was tested. Trabecular micro-architecture of tibia and L2 vertebrae (L2) and the cortical analysis of tibia were performed by 3D microtomography. Osteocalcin and CTX levels were assessed. At T0, the HF/HS diet group had developed a total and abdominal obesity and an impaired glucose tolerance compared with the Control group (p