A new bio-polymer based nanocomposite, pectin zirconium(IV) selenotungstophosphate (Pc/ZSWP) was prepared via sol–gel method. The material was characterized using scanning electron microscopy, X-ray diffraction, transmission electron microscopy and Fourier transform infrared spectroscopy. Distribution coefficient, thermal stability, elution behavior and pH titrations were investigated to explore the ion exchange behavior of nanocomposite. Pc/ZSWP exhibited higher ion exchange capacity (1.27meqg−1) than its inorganic counterpart (0.67meqg−1). To explore environmental applicability of the Pc/ZSWP, binary separation and selective separation of Cu2+ and Th4+ from synthetic mixtures of metal ions were achieved. Antimicrobial activity of the Pc/ZSWP was also investigated.