With increasing preference for all-natural foods to those involving synthetic chemicals, native isoelectrically precipitated soy protein isolate (SPI) was prepared using amaranth (Amaranthus tricolor L.) lye (pH > 12.5) and lemon extract, (pH < 2.5) as natural, food-plant-based chemicals. Protein content (91.21 %), yield (43.62 %) and digestibility correlation amino acid score (0.77) were obtained and were comparable to those of SPI prepared using synthetic chemicals (NaOH and HCl). Methionine and cystein-s were significantly higher in the natural SPI while glutamine and serine were higher in synthetic SPI (p < 0.01). Most of the determined minerals were higher in the natural SPI with potassium being the highest. Sodium was very high in the synthetic SPI. The rest of the minerals including phosphorus, iron and nickel, showed no significant difference. Anti-nutritional factors (trypsin inhibitors and phytic acid) were considerably lower in the natural SPI. Thus, a quality all-natural SPI can be produced using amaranth lye and lemon extract to address concerns regarding use of synthetic chemicals.