BACKGROUND: Prebiotics and probiotics may be effective dietary components that can alter the gut microbiota of the host and, consequently, overcome imbalances associated with obesity. This work aimed to evaluate the synergistic and isolated effects and mechanisms by which probiotic yogurt containing Bifidobacterium animalis and/or Lactobacillus acidophilus and yacon flour alter metabolic parameters and inflammatory and insulin signaling proteins in diet-induced obese mice. Swiss mice were fed a high-fat diet (n = 48) or a standard diet (control; n = 6) for 56 days. The 42 mice that gained the most weight were selected and divided into seven groups that received different combinations of probiotic yogurt and yacon flour. After 30 days, biochemical parameters (blood glucose, serum total cholesterol, and triacylglycerols), crude fat excretion in feces, and periepididymal fat were assessed and an immunoblotting analysis of insulin signaling proteins and interleukin-1⊎ was conducted. RESULTS:The combination of yacon flour and a yogurt with two strains of probiotics exerted positive effects on the parameters evaluated, such as decreased body weight (−6.5%; P < 0.05), fasting glucose (−23.1%; P < 0.05), and triacylglycerol levels (−21.4%; P < 0.05) and decreased periepididymal fat accumulation (−44.2%; P < 0.05). There was a decrease in inflammatory markers (P < 0.001) and an improvement in insulin signaling (P < 0.001). CONCLUSIONS:The combination of a prebiotic with two strains of probiotics in a food matrix may exert a protective effect against obesity-associated inflammation, improving insulin resistance, even in the short term.