Roots, cotyledons, leaves, stems, pods, and seeds of three soy cultivars were analyzed for their content of isoflavones, flavonols, coumarins, and phenolic acid derivatives with three samplings during a three-month period. The extracts were analyzed by HPLC/DAD and HPLC/MS, allowing us to confirm the presence of daidzein and genistein derivatives as the major isoflavones and to characterize coumarins, most flavonols and phenolic acid derivatives. Seeds exhibited the highest content of isoflavones: 12.61 g/kg of dry weight (DW) in cv. Emiliana; 8.97 g/kg of DW in cv. Elvir; 4.49 g/kg of DW in cv. Kure, and roots are the only part with coumarins, ranging from 4.08 g/kg of DW (cv. Emiliana) to 1.29 g/kg of DW (cv. Elvir) for the longest sampling period. Leaves, pods, and stems have flavonols, and in particular leaves showed: 7.28 g/kg of DW in cv. Emiliana; 6.57 g/kg of DW in cv. Elvir; 7.08 g/kg of DW in cv. Kure. The high content of isoflavones found in the seeds could be ascribed to the natural conditions under which the soy plants were grown.