Inorganic anions plays an important role in biological, industrial and environmental processes. Among the several anions, phosphate and nitrate ions are highly toxic and harmful to human health and the environment. Herein, we report the porous nature of the cerium incorporated chitosan-β-cyclodextrin (Ce-CS-β-CD) microspheres were prepared and systematically studied for their adsorption performance towards these toxic anions. The connection between the most substantial parameters such as agitating time, adsorbent dosage, co-interfering ions, pH as well as ionic strength with the adsorption percentage and capacity were optimized. The prepared microspheres were broadly characterized by XRD, EDAX with mapping images, SEM, FTIR, and TGA analysis. In the single component system, the adsorption performance showed that multilayer adsorption capacity of 88.54 and 72.12 mg/g for phosphate and nitrate ions respectively. The adsorption of the pseudo-second-order kinetic model showed a superior apt than the pseudo-first-order kinetic model can be effectively defined the uptake of kinetics. The thermodynamic parameters studies shows that the nature of the adsorption is feasible, endothermic and spontaneous nature. The feasible phosphate and nitrate adsorption mechanism of the prepared microspheres were ensued by ion-exchange, complexation and electrostatic interaction. Regeneration and reusability experiments were studied up to seven cycles by 0.1 M of NaOH as a regenerant to assess the reusability of the prepared microspheres. The aptness of Ce-CS-β-CD microspheres has been tested with field condition was investigated with industrial wastewater.