Zinc Oxide (ZnO) nanostructure doped with manganese (Mn: 5% and 10%) were prepared by the green synthesis method using the leaf extracts of Azadirachta indica. The microstructural investigation of the prepared nanopowders was carried out with the Rietveld refinement of the X-ray diffraction data. The phase analysis of the X-ray diffraction data confirmed that the synthesized nanoparticles have the hexagonal wurtzite structure in all cases. The Williamson Hall method was used to analyze the data obtained after the Rietveld refinement analysis to find some important microstructural parameters such as crystallite size, strain, stress and energy density. The size of the crystallites is almost the same in both cases and the values for strain, stress, and energy density increase with increasing Mn concentration. Functional groups and molecular interactions were identified by the Fourier Transform Infra-Red spectroscopy spectra. UV-visible spectra show that the band gap energy decreases with increasing Mn content. This property can help to fabricate a photodetector that can operate at a wavelength longer than the cut-off wavelength of ZnO. The morphology of the synthesized nanostructure was studied by field emission scanning electron microscope. The energy dispersive X-ray spectroscopy data confirm the elemental compositions in the synthesized Mn-doped ZnO, which means that the desired nanostructures were successfully synthesized by the green method.