Amaranth has been claimed as functional food, but its function on obesity-related disorder is not fully known. The aim of this study was to analyse the effect of amaranth protein intake on blood lipids profile and insulin resistance in diet-induced obese mice. The effect of soybean protein was also analysed for comparative purposes. C57BL-6 mice were fed for eight weeks with regular or high fat diet. Amaranth or soybean protein isolates (10 mg/kg) were supplied via oral administration. Changes in body weight, adipose tissue, total cholesterol, triglycerides, insulin, a glucose tolerance test, as well as the expression of lipid metabolism-related genes were measured. Our results have shown that amaranth protein induces a decrease in plasma insulin in mice fed with a regular diet, whereas a decrease in triglycerides was observed in mice fed with high fat diet. Furthermore, down-regulation of Tnf-α and Res, suggested the inhibition of inflammation state. The present study demonstrates that amaranth protein, but not soybean protein, improves the obese mice health, and the hormonal modulation (Lep, Fasn, Lpl) could lead to new mechanism of action by which amaranth consumption exerts its beneficial health effect.