Pomegranate peel (PP), a by-product of agro-food consumption, has a low adsorption capacity for nitrate and phosphate ions in aqueous media, but its surface is very rich in alcohol functional groups. In this work, the surface of pomegranate peels was functionalized by chemo-grafting 3-(2-Aminoethylamino) propyl] trimethoxy silane (AEAPTES) using the availability of alcohol groups to increase the adsorption capacity of the resulting adsorbent (PP/AEAPTES) towards nitrate and phosphate ions. The prepared PP/AEAPTES adsorbent was analyzed by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), Zeta potential, and X-ray photoelectron spectrometry (XPS). Under experimental conditions, the adsorption capacity of PP/AEAPTES has been found to be 124.57 mg/g and 94.65 mg/g for NO3− and PO43−, respectively, at pH 6 over a wide temperature range, and adsorption is exothermic for NO3− and endothermic for PO43−, as well as spontaneous and physical in nature. The adsorptions of NO3− and PO43− were also correctly described by the Langmuir isotherm and followed the pseudo-second-order model. The ability of PP/AEAPTES to adsorb NO3− and PO43− ions under real conditions was evaluated, and efficient regeneration and repetitive use of PP/AEAPTES was successfully achieved up to 5 cycles.