Pectin is one of the biopolymers in the cell walls of all plant tissues, but the pectin-containing materials have been discarded as industrial waste in food-processing factories. We prepared a water-insoluble pectin-inorganic composite material by mixing pectin and a silane coupling reagent, bis(3-trimethoxysilylpropyl)amine. The mechanical strength of the pectin-inorganic composite material was higher than that of the pectin material without the addition of an inorganic component. In addition, the thermal stability of the composite material increased with the addition of the inorganic component. Furthermore, when the pectin-inorganic composite materials were incubated in an aqueous solution of Cu(II), Zn(II), or In(III), these composite materials effectively accumulated not only the heavy metal ions, but also rare-earth metal ions. Additionally, based on the infrared (IR) measurements, the metal ion accumulative mechanism into the composite material is described. As a result, the IR spectra suggested an electrostatic interaction between the metal ion and carboxy group in the pectin.