In the present study, a toxic herbicide (glyphosate) was remediated through adsorption using biogenic conversion of amino-functionalized silica nanoparticles (silica NPs). The glyphosate adsorption and silica NPs were characterized using kinetics, isotherm and thermodynamics models, pH zero point charge measurements, BET surface analysis, X-ray diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscopy/energy-dispersive X-ray spectroscopy and regeneration study. The adsorption data were optimized by ANN multi-layer perceptron and multiple linear regression. The equilibrium glyphosate adsorption data were fitted to Freundlich, Langmuir, Temkin and Dubinin-Radushkevich (D-R) isotherm models. The adsorption capacity values recorded for the Freundlich and Langmuir models were 233.34 L/mg and 212.76 mg/g, respectively, at the maximum saturation dose. The fast rate-determining kinetics data were described by a pseudo-second-order model at different concentrations. The thermodynamics parameters clearly revealed that the adsorption of glyphosate was endothermic and spontaneous in nature. Finally, the optimized conditions were recorded as follows: initial glyphosate concentration 39.99 mg/L, pH 12.66, dose 0.299 g, contact time 60 min, and temperature 100 °C, with 98.99% removal. More importantly, the silicon NPs were easily recovered in different media, with acetic acid medium showing excellent regeneration. The present findings suggest that silicon NPs are a promising adsorbent for glyphosate removal from aqueous solutions.