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The impact of enzymatic treatment of Candida antarctica lipase B on a phenolics-rich extract from purple corn (Zea mays L.) (PCE) was evaluated. PCE was obtained by solid–liquid extraction with 80% ethanol. PCE was treated with lipase B in acetonitrile using octanoic acid as acyl donor for 72 h. Acylated and non-acylated PCE were tested for thermal stability at 80 °C, ɑ-glucosidase inhibitory activity, and molecular docking. The enzymatic treatment promoted the generation of a reaction product identified by HPLC along with a bathochromic shift (530 to 570 nm) in the extract. Enzymatic treatment increased (p < 0.05) the half-life of total anthocyanins in solution at 80 °C from 6.05 to 10.05 h. Additionally, enhanced (p < 0.05) the ɑ-glucosidase inhibitory activity at a concentration of 0.5 mg eq. C3G/mL (11.7% non-acylated and 33.2% acylated). Molecular docking using predicted acylated structures of major anthocyanins in PCE was correlated with biochemical evaluation on ɑ-glucosidase; for instance, cyanidin-3-(6″-n-octanoyl)-glucoside (−9.4 kcal/mol) had a more favorable binding energy than non-acylated cyanidin-3-O-glucoside (−8.4 kcal/mol) with the catalytic site of ɑ-glucosidase. A ligand–protein interaction analysis showed that the acyl group plays an important role in stabilizing anthocyanins in the catalytic cavity of ɑ-glucosidase. Our results suggest that treatment with lipase B is a promising strategy to improve technological and biological potential of pigments from purple corn. [ABSTRACT FROM AUTHOR]