The demand for plant-based ingredients is continuously increasing, but achieving optimal calcium and sodium supplies in plant-based food is a challenge. To this end, alternative fractionation processes were explored for the production of soy protein-rich fractions (soy protein concentrate), in which use of Ca(OH)2 instead of NaOH has been exemplified to produce high-calcium, low-sodium protein-rich fractions with adjustable functionalities. The use of Ca(OH)2 could lead to soy protein concentrates with a protein purity of 81% (with a conversion factor of 5.7). Further, it could lead to increased calcium content in the soy protein concentrate. Ca(OH)2 treatment decreased the solubility of the fractions from 89.7% to 8.6%, and enhanced their thermal stability and viscoelastic behaviour. The outcomes of this study could expand the applications of soy protein with suitable calcium and sodium levels.