Hesperidin (hesperitin-7-O-rutinoside) and hesperitin (hesperitin-7-O-glucoside) show anti-inflammatory, antimicrobial, antioxidant, and anticarcinogenic effects and prevent bone loss. However, hesperidin has a low bioavailability compared to hesperitin due to the rutinoside moiety attached to the flavonoid. The removal of the rhamnose group to yield the corresponding flavonoid glucoside (hesperetin-7-glucoside) improved the bioavailability of the aglycone, hesperetin, in humans. In line with these assumptions, the aim of this work was the enzymatic production of hesperitin from hesperidin with hesperidinase. Despite the low hesperidin solubility in the reaction medium, the enzymatic bioconversion was carried with hesperidin soluble at lower concentrations (≤0.05 mg ml−1) and insoluble for high concentrations (>0.1–50 mg ml−1). A twofold increase in maximum reaction rates overtook the expected values, pointing to the enzyme ability to degrade insoluble hesperidin. To improve the bioprocess, hesperidinase was tested soluble and immobilized in calcium alginate (2%), k-carrageenan (2%), and chitosan (2%) beads. The immobilization was carried out by adsorption and encapsulation. Chitosan was cross-linked with glutaraldehyde (1% and 2%) and sodium sulfate (13.5% and 15%) in acetate buffer (0.02 M, pH 4.0). The relation between bioprocessing conditions and hesperidinase stability was studied. A residual activity of 193% was obtained with immobilized hesperidinase compared to the soluble form. A half-life of 770 min was attained with hesperidinase encapsulated in calcium alginate beads. The results presented in this work highlight the potential of hesperidinase encapsulation towards hesperitin production with insoluble substrate. To our knowledge, this work presents for the first time the potential of hesperidinase encapsulation on hydrogels for hesperitin production. This is an important achievement for pharmaceutical and nutraceutical applications of hesperitin because this compound presents a higher bioavailability compared to hesperidin. Copyright © 2012 John Wiley & Sons, Ltd.