Diets high in fat can result in obesity and non-alcoholic fatty liver disease (NAFLD). The improvement of obesity and NAFLD is an important issue. β-Conglycinin, one of the soya proteins, is known to prevent hyperlipidaemia, obesity and NAFLD. Therefore, we aimed to investigate the effects of β-conglycinin on the improvement of obesity and NAFLD in high-fat (HF) diet-induced obese (DIO) mice and clarify the mechanism underlying these effects in liver and white adipose tissue (WAT). DIO male ddY mice were divided into six groups: HF, medium-fat (MF) and low-fat (LF) groups fed casein, and HF, MF and LF groups in all of which the casein was replaced by β-conglycinin. A period of 5 weeks later, the β-conglycinin-supplemented group resulted in lower body weight, relative weight of subcutaneous WAT, and hepatic TAG content (P=0·001). Furthermore, β-conglycinin suppressed the hepatic expression of Pparγ2 in the HF dietary group, sterol regulatory element-binding protein-1c and the target genes. The expressions of inflammation-related genes were significantly low in the epididymal and subcutaneous WAT from the mice fed β-conglycinin compared with those fed casein in the HF dietary group. Moreover, the expressions of Pparγ1 and Pparγ2 mRNA were suppressed in subcutaneous WAT in the HF dietary group but not in epididymal WAT. The concentrations of insulin and leptin were low in the serum of the mice fed β-conglycinin. In conclusion, β-conglycinin effectively improved obesity and NAFLD in DIO mice, and it appears to be a promising dietary protein for the amelioration of NAFLD and obesity.