The effect of synthesised IONPs employing a nontoxic leaf extract of Azadirachta indica as a reducing, capping, and stabilizing agent for increasing biogas and methane output from cattle manure during anaerobic digestion (AD) was investigated in this study. Furthermore, the UV-visible spectra examination of the synthesized nanoparticles revealed a high peak at 432 nm. Using a transmission electron microscope, the average particle size of IONPs observed was 30–80 nm, with irregular, ultra-small, semi-spherical shapes that were slightly aggregated and well-distributed. IONPs had a polydisparity index (PDI) of 219 nm and a zeta potential of −27.0 mV. A set of six bio-digesters were fabricated and tested to see how varying concentrations of IONPs (9, 12, 15, 18, and 21 mg/L) influenced biogas, methane output, and effluent chemical composition from AD at mesophilic temperatures (35 ± 2 °C). With 18 mg/L IONPs, the maximum specific biogas and methane production were 136.74 L/g of volatile solids (VS) and 64.5%, respectively, compared to the control (p < 0.05), which provided only 107.09 L/g and 51.4%, respectively. Biogas and methane production increased by 27.6% and 25.4%, respectively using 18 mg/L IONPs as compared to control. In all treatments, the pH of the effluent was increased, while total volatile fatty acids, total solids, volatile solids, organic carbon content, and dehydrogenase activity decreased. Total solid degradation was highest (43.1%) in cattle manure + 18 mg/L IONPs (T5). According to the results, the IONPs enhanced the yield of biogas and methane when compared with controls.