Even though fermented soybean (FS) contains various antioxidant compounds, this long-time processing still faces various oxidations caused by enzymes or heat. To elucidate the possibility of the oxidations as well as the level of enhancement of antioxidant properties to limit such oxidation, ergothioneine (ESH) concentrated extract (CE) from Aspergillus oryzae was used to interfere during FS processing. So, the supplementation of ESH CE (0%, 2%, 4%, and 6%) to one of three main stages such as soaking stage (SK), steaming (SM), or fermentation (FM) of the processing before measuring the quality changes of the final fermented product was done. The result showed that when added 4%–6% of ESH CE to the SK, ESH was slightly increased while 2,2-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activities and total phenolic compounds (TPC) increased considerably after fermentation by Bacillus subtilis. Total lipid was also slightly increased, whereas free fatty acid (FFA), peroxide value (PV), and thiobarbituric acid reactive substances (TBARs) decreased sharply compared with the control sample. Although supplemented at SK, L^*-value increased sharply from 0% to 4% and then decreased slightly at 6% of ESH CE, higher than at SM, and subsequent FM, ∆E-value and a* and b* value changed in the opposite direction when these parameters decreased the sharpest at SK, lower than at SM and then at FM. The results indicate that supplementing with 4%–6% ESH CE at the early SK of FS processing shows a compatible difference with other stages, not only helping to prevent lipid oxidation but also improving the bright color of the final FS.