The present study aimed to investigate the influence of microwave irradiation on the physical and functional properties of starch extracted from Nelumbo nucifera seed flour. The seed flour was obtained by manual grinding of seeds and irradiated at different microwave treatment time, i.e., 1, 2, 3, 4 and 5min at the low-medium intensity. The starch was extracted in distilled water and dried at room temperature using a vacuum desiccator. The morphology, crystal structure, and surface parameters of starch granules were analyzed using scanning electron microscopy, X-ray diffraction, Fourier transform infra-red spectroscopy and Brunauer, Emmett and Teller surface analysis techniques. The functional properties of starch were also determined in terms of water and oil holding capacity, swelling capacity, emulsifying activity and gelling ability. Evidently, crystallinity, surface area and pore volume of starch granules were found to be increased, while particle size and average pore size were decreased as a function of microwave treatment time. The microwave-induced variations in physical parameters significantly affected the functional properties of starch. A significant (p>0.05) exponential decrease in extraction yield and gelling ability, while an exponential increase in the functional properties of starch with increase in the microwave treatment time (R2=0.915–0.985) was recorded.