Rice husk is a lignocellulosic biomass rich in silica, which, when disposed of inappropriately, represents an environmental hazard. This study investigated the application of deep eutectic solvents (DES) as a green and efficient approach to the rice husk fractionation, combining the selective dissolution of lignin and sugars with the purification of the silica-rich inorganic fraction. Six different DES were produced from choline chloride or betaine with different hydrogen bond donors and characterized for water content and pH. The DES based on carboxylic acids was more acidic, which favored the cleavage of ester and glycosidic bonds in the biomass. The TGA, XRF, SEM, and XRD analyses revealed that the lactic acid-based DES promoted better removal of lignin and mineral impurities, resulting in a purer silica with an amorphous morphology. The 110 °C condition was the most effective in preserving the thermal integrity of the organic (sugars and lignin) and inorganic (silica-rich ash) fractions. The results highlight the potential of DES as selective, sustainable, and tunable solvents for the valorization of agricultural waste, achieving biosilica with SiO₂ purity exceeding 80% and lignin removal above 70%, reinforcing the potential of DES as sustainable solvents for agricultural waste valorization.