Black garlic (BG) is a functional food derived from fresh garlic (FG) that has a significant antioxidant activity (AOA). Little is known about the influence of FG composition on the antioxidant properties of BG. Therefore, we used seven different FG cultivars to produce BG, and monitored changes in basic composition, metabolomic profile and AOA. We found that different cultivars and the ageing process significantly impacted most of the markers. On average, 27 markers were upregulated, 21 downregulated, and 26 remained unchanged or changed to a lesser degree. Correlation study revealed that fructosyl-arginine positively associates with AOA of BG (r = 0.8, p < 0.05 for ABTS). Moreover, fructosyl-arginine in BG correlates with protein content (r = 0.79, p < 0.05). Thus, crude protein content in FG may serve as a practical predictor of the AOA of BG under the tested conditions. This study presents a deeper understanding of tailoring the BG biological potential.