Passion fruit peel contained various phenolic compounds with α-glucosidase and α-amylase inhibitory activities in vitro. However, the bound state and glycosylated forms hindered their active expression. In this article, β-glucosidase-producing Lactobacilli were inoculated into fermented peels for targeted metabolism. The results showed that the release of bound polyphenols and the increase of free polyphenols were significantly correlated with β-glucosidase activity. The strain G1 with high enzyme activity degraded 48.20% of the bound polyphenols after 24 h. The ability of extracts to inhibit α-glucosidase and α-amylase activities was significantly enhanced and closely related to the content of free polyphenols (r = −0.96 and −0.88, P < 0.001). Computer-assisted screening identified 38 phenolic compounds as potential dual inhibitors of α-glucosidase and α-amylase. Among them, 22 α-glucosidase inhibitors and 24 α-amylase inhibitors were identified for the first time. Various inhibitors, including phenolic acids, flavones, and flavonols, increased in content after fermentation. The total content of 14 glycosylated polyphenols decreased to 28.38% at 48 h, which was opposite to the aglycone. Molecular docking indicated that glycosylated polyphenols bind to β-glucosidase through hydrogen bonds and van der Waals forces. Different glycosylations at the C-3 position of quercetin bound at same sites to β-glucosidase. This study contributes to the theory of enhancing the functional activity of natural products through targeted fermentation transformation.