The study was focused on determination of the effect of cool storage on the polyphenol profile and antioxidant capacity of potentially bioaccessible phenolics from control and probiotic-rich soybean sprouts. Malonyl glycitin and malonyl genistin were found to be the dominant isoflavones in the sprouts. The contents of the isoflavones after cold storage were generally equal or higher than in the fresh sprouts. The highest reducing power was determined for the potentially bioaccessible fraction from the probiotic-rich sprouts (9.9 mg TE/g, approx. a 4-fold increase compared to the control). The storage positively influenced the reducing potential; after gastric digestion, there was a 61% and 59% increase for the control and probiotic-rich sprouts, respectively. The addition of probiotic bacteria did not increase the phenolic content; however, it improved the antioxidant capacity. Importantly, the antioxidants in the proposed sprouted food were characterized by high storage stability. Soybean sprouts enriched with L. plantarum can be recommended for consumers who prefer new functional foods with pro-health properties.