The objectives of this research were to demonstrate the changes in isoflavone-aglycones, total phenolics, and biological properties (digestive enzyme inhibition; antioxidant) from six organs including leaves, leafstalks, roots, stems, seeds, and pods at different growth times of soybean plant. Three isoflavone-aglycones in microwave-assisted acid hydrolysis extracts were elucidated using UHPLC-ESI-Q-TOF-MS/MS and their contents exhibited remarkable differences in leaves (245.93-2239.33 μg/g), roots (854.96-4425.34 μg/g), and seeds (ND-2339.62 μg/g). Specifically, the collected samples on 15-Oct (leaves: 2239.33; seeds: 2339.62 μg/g) and 31-Aug (roots: 4425.34 μg/g) showed the highest isoflavone-aglycones, and daidzein was observed the most abundant component, comprising approximately 70%. Moreover, the inhibitions against α-glucosidase and α-amylase displayed the predominant effects in roots (89;91%) and leaves (81;85%) of samples on 31-Aug and 15-Oct at 300 μg/ml. The antioxidant activities on ABTS, DPPH, and hydroxyl radicals increased considerably with the increases of growth times in leaves and seeds, especially, ABTS showed the highest scavenging abilities: leaves (15-Oct;83%) > roots (31-Aug;75%) > seeds (15-Oct;68%). Therefore, our results suggest that soybean leaves, roots and seeds may be considered as excellent natural sources for nutraceuticals.