Yacon flour has been considered a food with prebiotic potential because of the high levels of fructooligosaccharides, which allows for its use in formulating synbiotic foods. The purpose of this study was to evaluate the effect of yacon flour and probiotic (Bifidobacterium longum) on the modulation of variables related to bone health. Thirty-two Wistar rats were divided into 4 groups: control, yacon flour, diet+B. longum, and yacon flour+B. longum. After euthanasia, the bones were removed for analysis of biomechanical properties (thickness, length, and strength of fracture) and mineral content (Ca, Mg, and P); the cecum was removed for analysis of the microbiota and short-chain fatty acids. Tibia Ca, P, and Mg content was significantly (P<.05) higher in groups fed diet+B. longum, yacon flour+B. longum than in the control group. An increase in fracture strength was observed in the yacon flour (8.1%), diet+B. longum (8.6%), and yacon flour+B. longum (14.6%) in comparison to the control group. Total anaerobe and weight of the cecum were higher (P<.05) in rats consuming the yacon flour diet compared with the other groups. Cecal concentration of propionate was higher in all experimental groups compared with the control (P<.05). Yacon flour in combination with B. longum helped increase the concentration of minerals in bones, an important factor in the prevention of diseases such as osteoporosis.