The protective role of kodo millet whole grain and bran supplementation in diet induced obesity has not been investigated. Here we have studied the role of kodo millet supplementation in age matched Swiss albino mice that were randomly divided into groups and fed their respective diets for 16 weeks. A high fat diet increased weight gain, reduced glucose tolerance, increased serum lipids, altered hepatic and adipocyte gene expression and caused dysbiosis in the intestinal beneficial bacteria. Kodo millet supplementation did not affect weight gain but it improved glucose tolerance and prevented an increase in the serum cholesterol and lipid parameters (P ≤ 0.05), modulated adipogenesis related gene expression, decreased serum IL-6 and LPS levels (P ≤ 0.05), promoted selected beneficial gut bacterial abundances (Lactobacillus sp., Bifidobacteria, Akkermansia and Roseburia spp.) and improved the total short chain fatty acid production (P ≤ 0.05) and acetate levels (P ≤ 0.05) in cecal contents. This study provides evidence that kodo millet supplementation alleviates high-fat diet induced changes and hence can be incorporated as a functional ingredient for the management of obesity.