In this study we investigate the effect that Agave fructans as new prebiotics have on mineral absorption improvement. Forty-eight 12-week-old C57BL/6J mice were used in this study. Forty mice were ovariectomized and eight were sham-operated controls. Mice were fed standard diets or diets supplemented with 10% Agave fructans or 10% inulin fructans. Calcium and magnesium were evaluated as well as their excretion in feces. Osteocalcin levels were also measured; femur structure was studied by scanning electron microscopy. Other parameters, such as food intake, body weight, glucose, and short-chain fatty acid content, were recorded. Calcium in plasma and bone increased in Agave fructan groups (from 53.1 to 56 and 85 mg/L and from 0.402 to 0.474 and 0.478 g/g, respectively) and osteocalcin increased in all fructan groups (>50%). Scanning electron microscopy showed that fructans were able to mitigate bone loss. In conclusion, we demonstrated that supplementation with Agave fructans prevents bone loss and improves bone formation.