Abstract Bariatric surgery induces a decrease in areal bone mineral density (aBMD), but the long-term effect on trabecular and cortical volumetric bone mineral density (vBMD) has not been well assessed. The main aim of this 5-year longitudinal study was to investigate the changes following sleeve gastrectomy (SG) in aBMD, bone turnover markers and trabecular and cortical vBMD. Forty-five patients with obesity were assessed before and 1, 2 and 5 years after SG. Trabecular and cortical vBMD, cortical thickness and structural parameters were assessed by 3D-Shaper® software at hip. Values of bone turnover markers peaked after 1 year and decreased after 2 and 5 years, but without returning to baseline values. aBMD decreased mostly at femoral neck(-9.7%) and total hip(-10.7%) over the 5 years, with the greatest loss occurring at 1 year(-5.9% and -6.3%, respectively). A similar profile of decrease was observed for integral hip vBMD with significant decreases of 6.6%, 7.7% and 10.7% after 1, 2 and 5 years, mainly due to a reduction in the trabecular (10.5%, 12.0% and 17.2%, respectively) rather than cortical (1.4%, 1.9% and 2.9%, respectively) component. A modest decrease in mean cortical thickness (2.5%, 2.8% and 3.9%, respectively) and an alteration in the structural parameters were concomitantly observed. Older age and greater body weight loss were the factors most associated with an increased loss of aBMD and vBMD. In conclusion, the study demonstrates that SG induces not only an alteration in bone turnover and aBMD, but also a reduction in vBMD at hip, predominantly due to trabecular component deterioration as determined by 3D-Shaper® software. The maintenance of bone deterioration for at least 5 years – that is, after 4 years of relative body weight stabilization or minimal weight regain − suggests the need for a therapeutic approach to preserve bone health in patients who undergo SG.