In recent days, the synthesis of nanoparticles using biomaterials is growing very rapidly due to their non toxicity and eco friendliness. In the present study we demonstrated the role of individual organic compounds present in the plant extracts in the synthesis of silver nanoparticles (Ag NPs) using Karanjin, a natural flavonoid extracted from seeds of Pongamia pinnata L. assisted by microwave technique. The plasmon resonance absorbance peak was observed at 424 nm in UV–visible spectroscopy. The TEM results showed presence of spherical shape with ~20 nm in size. The FTIR spectrum indicates there is no organic molecule present in the powder material and it confirms the formation of Ag NPs by microwave method. Further, confirmed by X-ray diffraction (XRD) and Energy Dispersive Spectroscopy (EDS) analysis. AFM images explained the topography of the Ag NPs. The obtained nanoparticles were stable and it confirms the activity of Karanjin as a reducing and capping agent in synthesis of Ag NPs. The synthesized Ag NPs demonstrated good antifungal activity against Aspergillus flavus and A. niger.