In this study, soy-powder yogurt (SPY) with enhanced levels of γ-aminobutyric acid (GABA) and isoflavone aglycone was produced from sprouting high-protein soybeans (HPSs). The fermented steam-HPS sprouts (0 to 4 cm) were fermented (72 h) with Lactobacillus brevis, and the total free amino acids (FAAs) of the formed mixtures were determined to be 79.53, 489.93, 877.55, 780.53, and 979.97 mg/100 mL in the fermented HPS (FHPS), and the fermented steam-HPS with 0 cm (FSHPS-0), 1 cm (FSHPS-1), 2 cm (FSHPS-2), and 4 cm sprouting lengths (FSHPS-4), respectively. The levels of glutamic acid (GA) and GABA were observed to be the highest, 100.31 and 101.60 mg/100 mL, respectively, in the unfermented HPS (UFSHPS-1, 1 cm) and FSHPS-1 sprouts, respectively. Moreover, the total contents of the isoflavone glycoside form decreased proportionally to the increasing total levels of isoflavone aglycones after fermentation in FSHPS-0, FSHPS-1, FSHPS-2, and FSHPS-4. The levels of isoflavone aglycones were detected as 350.34, 289.15, 361.61, 445.05, and 491.25 μg/g in FHPS, FSHPS-0, FSHPS-1, FSHPS-2, and FSHPS-4, respectively. While FSHPS-1 exhibited the highest DPPH (63.28%) and ABTS (73.28%) radical scavenging activities, FSHPS-4 contained the highest isoflavone aglycone ratio (81.63%). All in all, the FSHPS-1 mixture prepared in this study exhibited high GABA content and functional prosperity, thereby making it suitable for potential applications in the soy-dairy industry.