In the present study, biosynthesized silica-based zinc oxide nanocomposites (nano-SZO) have been explored as nanoadsorbent for sequestrating heavy metal ions viz. Ni2+, Cd2+ and Cu2+ from synthetic medium. The nanocomposites have been obtained by utilization of agricultural waste by means of green synthetic approach with an average particle size of 30.52 nm and a pH at zero-point charge as 4.8. The process has been optimized at a pH equal to 5.0 for Ni2+ and 6.0 for Cu2+ and Cd2+. Adsorption was best described by Langmuir isotherm and the highest value of maximum adsorption capacity, qm of nano-SZO was obtained for Cu2+ (32.53 mg/g), Ni2+ (32.10 mg/g), and Cd2+ (30.98 mg/g). The studied heavy metal ions are considerably adsorbed by the nano SZO through chemisorption by active binding with polyhydroxy functionalities attached at the surface of the nanoadsorbent. Thus, the biosynthesized nano-SZO can be utilized as eco-friendly and efficient nano adsorbents for the sequestration of heavy metal ions.