With rising environmental and human health concerns, the development of wood adhesives has shifted from petrochemical feedstocks to low-cost biobased feedstocks. Here we report a novel approach to prepare a sustainable and environmentally friendly soy adhesive. A low-cost fermentation broth of Aspergillus niger contained an enzyme complex that showed excellent performance in hydrolyzing polysaccharides in defatted soy flour (DSF). Efficient hydrolysis of polysaccharides in DSF by this enzyme complex was proved by the increased reducing sugar concentration in hydrolysate, the decreased content of water-insoluble substances, and the weakened rheological properties of the slurry. It was further demonstrated that the resultant hydrolysate, namely, reducing sugars, could be cross-linked with soy protein, based on the thermogravimetric analyses, Fourier-transform infrared spectroscopy, atomic force microscopy nanomechanical mapping, and sol–gel tests. With the self-cross-linked structure, the enzyme-treated soy adhesive had significantly improved adhesive strength and water resistance as compared to that without the enzymatic hydrolysis. Particularly, the wet bonding strength of two-layer plywood increased by over 30%, showing great potential for preparing all-biomass composite materials in an industrial scale.