The use of microwave irradiation energy for isolating bioactive compounds from plant materials has gained popularity due to its ability to penetrate cells and facilitate extraction of intracellular materials, with the added benefits of minimal or no use of organic solvents. This is particularly significant due to the possibility of using extracts in the food and pharmaceutical industries. The aim of this work is to examine the effect of microwave irradiation on the extraction of three of the most important isoflavones from soybean flour, glycitin, genistin, and daidzin, as well as their aglycones, glycitein, genistein, and daidzein. By varying the extraction time, temperature, and microwave power, we have established the optimal parameters (irradiation power of 75 W for 5 min) for the most efficient extraction of individual isoflavones. Compared to conventional maceration and ultrasound-assisted extraction, the total phenol content of the extracts increased from 3.66 to 9.16 mg GAE/g dw and from 4.67 to 9.16 mg GAE/g dw, respectively. The total flavonoid content increased from 0.38 to 0.83 mg CE/g dw and from 0.48 to 0.83 mg CE/g dw, and the antioxidant activity increased from 96.54 to 185.04 µmol TE/g dw and from 158.57 to 185.04 µmol TE/g dw, but also from 21.97 to 37.16 µmol Fe2+/g dw and from 30.13 to 37.16 µmol Fe2+/g dw. The positive correlation between microwave extraction and increased levels of total phenols, flavonoids, and antioxidant activity demonstrates the method’s effectiveness in producing bioactive compounds. Considering the growing recognition of glycitein’s potential role in medical and pharmaceutical applications, microwave-assisted extraction under optimized conditions has proven highly efficient.