New antifungal agrochemicals compounds discovering from natural products are a vital goal for the management of plant pathogenic fungi. As present synthetic fungicide used for the treatment of plant pathogenic fungi have negative effects on environment and human health. Therefore, it is need of the day to develop and discover new antifungal substances from natural products. The objective of the current study was to evaluate the extracts of leaves, seeds and twigs of Azadirachta indica using infusion, decoction and microwave extraction techniques. These extracts were subjected to phytochemical quantification, Fourier Transform Infrared (FTIR) spectroscopic analysis and antifungal assays against pathogenic fungi by well diffusion technique. The quantitative of phytochemicals screening showed that leaves had showed high concentrations of bioactive compounds, seeds showed a moderate and twigs observed the least phyto-compounds. The infusion extracts system showed high amount of active compounds, followed by microwave and decoction. Extracts of leaves and seeds showed evidence of inhibition growth of fungi. The spectra of FTIR verified the occurrence of different functional groups such as aromatic compounds, alkanes, alkyl halides, amines, carboxylic acids, phenols, alcohol and amino acids, in the neem extracts. Relevant stakeholders along with the help of policy makers and researchers should build extra understanding regarding the requirement to clinch products of organic fungicides like secure fungus management system.