In this study, we created biocatalytically coated porous starch granules (PSGs) using amylosucrase from Neisseria polysaccharea to apply them as an encapsulant for target-specific delivery. Field-emission scanning electron and confocal laser scanning microscopic images showed that the PSGs were completely concealed by the alpha-glucan coating layer. This carbohydrate-based encapsulant displayed higher amount of resistant glucan contents due to the elongated chains of the glucan coating, resulting in lower digestibility of these PSGs in simulated digestive fluid systems. Among the various PSGs evaluated, the highest loading efficiency for the bioactive molecule crocin was observed with the beta-amylase-induced PSGs (beta-PSGs) that had the smallest nanosize pores. Furthermore, alpha-glucan-coated beta-PSGs showed the highest capacity to preserve the loaded crocin when incubated in simulated digestive fluids. This suggests that the alpha-glucan-coated beta-PSGs can potentially be used for the delayed release of the core material in the upper region of the gastrointestinal tract. Therefore, this system can be potentially utilized as an effective carrier for colon-specific delivery, and the release of the bioactive compound can be triggered by beneficial intestinal microbiota.