This study was conducted to develop functional black soy sauce with (S2) and without (S3) an outer skin and then compare these products to a control soy sauce (S1). In addition, the effects of different fermentation periods on the pH, buffering power, titratable acidity, total acidity, salt content, and browning and Lab value were evaluated. Furthermore, the antioxidative activities of the black soy sauce were compared to those of the control soy sauce based on the total phenolic compounds and free radical scavenging activity, including the 1,1-diphenyl-2-picryl-hydrazil (DPPH) scavenging activity and the thiobarbituric acid value (TBA value). The pH and buffering power of S2 were lower than of S1 and S3, while the titratable acidity and total acidity were higher. The salt content of all samples decreased after 60 days of fermentation, after which it increased slightly for up to 180 days. Additionally, the browning intensity of all samples increased as the fermentation periods increased, with the browning intensity at 420 nm of S1 being the highest followed by S3 and S2. After 150 days of fermentation, the L value of S1 was higher than that of S2 and S3, but the while a value of S2 was higher than those of S1 and S3 and was increased as the fermentation periods. Moreover, the b value of S1 was the highest at the end of the fermentation period, followed by the b values of S3 and S2. The amount of total phenolics in S1 was greatest, followed by S2 and S1. Conversely, the DPPH radical scavenging activity of S2 was the highest, followed by S3 and S1. Finally, the TBA value increased rapidly from day 30 to day 180 of the fermentation period, and the TBA value of S2 was lower than those of S1 and S3.