Isoflavonoid composition of freshly harvested soy sprouts of six cultivars grown in Colombia was analyzed. Evaluations on the effect of storage time at 12 °C and exogenous application of the elicitor 2,6-dichloro isonicotinic acid (INA) were carried out to establish their influence in the ability of soy sprouts for synthesizing isoflavonoids. In addition, elicited and non-elicited sprouts of soy cultivar Soy SK-7 was assessed for total phenolic content and antioxidant activity according to the growth stage (VE, VC, and V1) and tissues (cotyledon-epicotyl and hypocotyl-root). Isoflavonoid content and antioxidant capacity were dependent on the cultivar, growth stage, tissue, and storage time at 12 °C. Growth stages VE and V1 and the hypocotyl-root exhibited the highest total phenolic content and antioxidant activity. In general, 6”-O-malonylgenistin, daidzin and genistin were the major constituents in the cultivars. Soy SK-7 and Panorama 358 displayed the highest amounts of 6”-O-malonylgenistin (155.9 µg/g) and daidzin (83.5 µg/g), respectively. Results showed that the isoflavonoids and phenolic contents and antioxidant activity were significantly increased by application of INA. This information can be useful to produce soybean sprouts with increased amounts of bioactive compounds and improved response to abiotic and biotic stresses.