Water-soluble soy protein (SP), which contains many acidic amino acids in its structure, was complexed by mixing with a silane coupling agent, 3-glycidoxypropyltrimethoxysilane (GPTMS). These SP−GPTMS composite materials showed stability in water. This property is due to the cross-linking between SP and GPTMS through the ring cleavage reaction of the epoxy group in the GPTMS molecule and an encapsulation of SP into the 3D siloxane network of GPTMS. When the SP−GPTMS composite material was immersed in an aqueous Cu(II) ion solution, the composite material changed from light brown to blue green by the coordination of Cu(II) ions into the SP. Hence, we evaluated the accumulation of heavy ions, rare-earth ions, and light metal ions. The accumulating affinity of metal ions was Cd(II) << Zn(II), Cu(II), Pb(II) < La(III) < Al(III) < Nd(III), In(III) << Mg(II) < Ca(II) ions. In addition, the sorption capacities of Ca(II), Mg(II), In(III), Nd(III), Al(III), La(III), Pb(II), Cu(II), Zn(II), and Cd(II) ions were 700 nmol/mg, 660 nmol/mg, 470 nmol/mg, 470 nmol/mg, 410 nmol/mg, 380 nmol/mg, 350 nmol/mg, 350 nmol/mg, 300 nmol/mg, and 200 nmol/mg, respectively. These properties suggest that the SP−GPTMS composite material has a divalent light metal ion selectivity. Additionally, the accumulative mechanism of the light metal ions was related to the carboxylate group and the hydroxyl group in the composite material.