Abstract Herein, a bio-inspired, environmentally benign synthetic strategy has been developed for CuSnO3 quantum dots and its photocatalytic efficiency towards degradation of Rabeprazole has been investigated. The synthesized nanomaterials were characterized by UV–Vis, XRD, XPS and TEM techniques. The elliptical CuSnO3 QDs have sizes less than 3.8 ± 0.3 nm. The results of photocatalytic degradation of Rabeprazole under solar irradiation revealed the synergistic effect of double oxide nanoheterojunction. The kinetics of the photodegradation process was found to be of pseudo first order with rate constant 6.3 × 10−2 min−1. The effect of pH on the degradation efficiency and reusability of the catalyst were also thoroughly investigated. The degradation products have been identified using HRLCMS technique and degradation pathway has been proposed. The sunlight harvesting capability of tuned band structured CuSnO3 QDs have lead to the efficient degradation of Rabeprazole under solar irradiation.