Obesity is defined as abnormal or excessive body fat accumulation that may have negative effects on health. Healthy diet induces a balance of gut microbiota, helping in turn to combat this metabolic disorder. Amaranth is well known because of its beneficial properties on health, but its effects on microbiota profile are still unknown. The aim of this study was to analyse the changes of gut microbiota in diet-induced obese mice due to amaranth protein consumption and to compare them with the changes due to soybean protein intake. Male C57BL/6 mice were fed for 8 weeks with regular (RD) or high-fat (HF) diet, without or with complementation with amaranth or soybean protein isolates. Morphological changes in caecum ultrathin sections were measured after hematoxylin/eosin staining. Microbiota was isolated from the caecum and 16S rRNA gene was sequenced. Caecal Short Chain Fatty Acids (SCFAs) were quantified by gas chromatography. The consumption of soybean protein induced the ectopic deposition of fat in the whole intestine while amaranth proteins increased caecal crypt depth and calceiform cells number sustaining its beneficial effect on health. The count of Ruminococcacea family bacteria was increased in mice fed with HF diet, but amaranth proteins intake reduced its abundance. In turn, Lachnospiraceae bacteria abundance decreased in mice fed the Control-HF and amaranth HF diets, but increased in mice fed the soybean diets. In mice fed the RD diets, amaranth induced the abundance of Prevotellaceae, an acetate-producing bacteria. Study results indicate that the modulation of caecal microbiota could be one of the mechanisms by which amaranth exerts its beneficial effects on health.