Basic yellow 28 dye, used extensively in the textile and leather industries, poses significant environmental and health risks, including allergic reactions, skin irritation, and respiratory problems. This study reports the Pechini sol-gel synthesis of novel ZnO/Mg3B2O6 nanostructures for the decontamination of basic yellow 28 dye from aqueous solutions. The nanostructures were synthesized by calcining at 650 and 850 °C for 5 h, producing ZM650 and ZM850, respectively. The average crystallite sizes were 39.28 nm for ZM650 and 51.03 nm for ZM850. BET surface areas were 70.71 m2/g for ZM650 and 48.13 m2/g for ZM850. FE-SEM and HR-TEM analyses revealed distinct morphological structures, with ZM650 exhibiting a dense aggregation of rod-like particles and ZM850 showing larger clusters. The maximum adsorption capacities were 381.68 mg/g for ZM650 and 303.03 mg/g for ZM850. The optimum adsorption was observed at a pH of 10, a contact time of 70 min, and a temperature of 298 K. Regeneration using a 6 M HCl solution demonstrated efficient reusability over five cycles. The adsorption process followed pseudo-second-order kinetics and the Langmuir isotherm, indicating monolayer adsorption. Also, the adsorption process was found to be physical and exothermic.