Tofu protein composition changes induced by a pilot plant processing method involving hydrothermal cooking, commercial rennet as coagulant and inulin as functional ingredient were assessed. Glycoproteins (γ-, β-conglycinin) were firmly bound to the matrix of the obtained gels. Extractable proteins of inulin-enriched tofu were with mainly basic 7S-globulin, and polypeptides of glycinin. Polypeptides A1,2,4 and B1,2,4 were found in higher concentrations in protein extracts of tofu than other 11S polypeptides. Tofu was characterized by high total (417.6–556.5 g/kg) and extractable soluble (155.3–367.5 g/kg) protein content, good protein extractability (37.2–68.6%), both total protein (52–69%) and soluble protein (50–76%) recovery. Increasing concentrations of inulin proportionally improved tofu hardness (6.23–8.98 N/cm2) contributing to the uniformity of gel microstructures. Inulin played an important role in incorporating β- and γ-conglycinins into the gel matrix and by increasing the concentration of inulin in soymilk before gelation, the content of extractable soluble proteins, protein extractability and soluble protein recovery of produced tofu were also proportionally increased. For all tested sensory attributes the grades were increased with increasing inulin content in the samples. Under the applied production method, protein composition and proportion of inulin had important roles in defining tofu quality.