Starch enzymatic hydrolysis is a key technology for preparing plant-based dairy alternative beverages, preferred for its low energy consumption, high product yield, and quality. However, the high-temperature requirement to terminate reactions and challenges in continuous operations hinder enzyme applicability. Therefore, encapsulation techniques have been explored to address these limitations, enhancing the enzyme’s stability and facilitating process control. This study developed a novel amyloglucosidase encapsulation system based on chitosan-SDS hydrogel capsules produced by simple coacervation. The enzymatic activity of free and immobilised amyloglucosidase was assessed using corn starch and maltose as substrates. The encapsulation process successfully yielded self-supporting structured and spherical capsules, achieving an immobilisation yield of 71% and an enzyme efficiency of 83%. The residual enzymatic activity after 28 days of storage remained at 76%. A feedback inhibition investigation was performed by varying the concentration of corn starch, and favourable applicability of encapsulated amyloglucosidase for continuous processes was found. The encapsulation process offered several advantages, such as a straightforward separation step to halt enzymatic reactions and no need for high temperatures that may affect food product attributes. Lastly, the amyloglucosidase-chitosan-SDS coacervates show promise in improving enzyme stability, facilitating hydrolysis control, and expanding enzyme utilisation in dairy alternative plant beverage manufacture.