The malachite green (MG) is very difficult to degrade in water; thus, it needs an efficient photocatalyst. In this study, neem extract was used to tune the surface and crystal properties of ZnO nanostructures for the photodegradation of MG. The biosynthesized ZnO samples were prepared by hydrothermal method in the presence of 5, 10 and 15 mL of neem extract. The structural characterization has shown nanoparticle like morphology of ZnO as revealed by scanning electron microscopy (SEM) and hexagonal phase was confirmed by powder X-ray diffraction (XRD) technique. The XRD analysis has shown a shift in the 2 theta towards lower angle for ZnO with increasing amount of neem extract. Also, the crystallite particle size of ZnO was decreased with increasing neem extract. The UV-visible spectroscopy has shown the decrease in the optical band gap of ZnO, and the lowest band gap is possessed by ZnO sample produced with 15 mL of neem extract. The ZnO sample obtained with 15 mL of neem extract has shown approximately 99% degradation efficiency for MG for 70 min in aqueous solution. The superior photocatalytic activity of ZnO sample with 15 mL of neem extract could be attributed from the decrease in charge recombination rate due to the decreased optical band gap and particle size.