Microwave (MW) treatment is a promising technique in cereal processing to improve nutritional quality. The present study investigated the effect of MW power level and exposure time on white finger millet flour (WFMF). Nine different MW treatment combinations were taken based on power level (720 W, 840 W, and 900 W), and exposure time (2 min, 4 min, and 6 min), after the MW treatment the flours are stored at 45 C for 15 days for storage study. The physicochemical, functional, pasting properties, and storage stability of the treated flours were analyzed. According to the results of the study, MW power level and exposure time significantly (p < 0.05) affected the color, swelling power, and water and oil absorption index. The MW treatment reduces the free fatty acid (FFA) and peak viscosity of the samples. The storage study for up to 15 days reveals the changes in color, FFA, and pasting properties of the sample. During storage, the change in FFA content was higher in control untreated flour (CF) than MW treated samples. Due to the structural changes in the starch molecules, the viscosity of MW treated samples was reduced drastically than the CF sample. Results denote that both MW power level and exposure time had a significant effect to alter the functionality and storage stability of WFMF. Practical ApplicationsWhite finger millet (WFM) is the major raw material used for numerous cereal-based products. Microwave (MW) treatments are a novel and promising technology used in cereal processing. A study on changes in finger millet properties under MW treatment helps to improve/alter the functional properties of millet flour, which can be used in new product development. Based on the study, MW treatment significantly improves storage stability by reducing the free fatty acid content, so MW treatment can be used to maintain the quality of the WFM during the storage period to minimize storage losses.