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Soybean is a rich source of bioactive compounds, such as phenolic acids, flavonoids, isoflavones, carotenoids, and tocopherols. The amount of bioactive compounds in freshly harvested soybeans and their derived products has been determined; however, when they are used in the food industry, soybeans are generally stored prior to being processed. This study aimed to evaluate the effects of soybean moisture content (12%, 15%, and 18%) and storage temperature (11, 18, 25, and 32 °C) on the free phenolic, total flavonoid, vanillic acid, total carotenoid, and δ- and γ-tocopherol content of soybeans stored for 12 mo. Moreover, the ABTS and DPPH radical scavenging activities of phenolic extracts were determined. There was an increase in free phenolics and total flavonoids in the stored grains compared with the grains on the 1st d of storage. Vanillic acid showed a decrease in soybeans stored at 15% and 18% moisture content and 25 or 32 °C, which indicated some degradation into other metabolites. Total carotenoid content decreased as a function of storage temperature and showed some temperature-dependent degradation. The δ- and γ-tocopherol content also tended to decrease in grains stored at 15% or 18% moisture content or 25 or 32 °C, regardless of the moisture content studied.