This study evaluated the use of enzymatically synthesized dextran nanoparticles to entrap a hydrophobic nutraceutical, the isoflavone genistein. The focus was on the synthesis of pure dextran as the material for the entire nanoparticle, and their inclusion-complexation of genistein. Under optimal conditions (pH 5.2–6 and sucrose concentration >0.5 M), dextransucrase generated spherical dextran nanoparticles (100–450 nm). The two nutraceutical inclusion methods were DMSO dilution in water and acidification. Optimization of the inclusion processes produced nanosized dextran particles containing genistein. The DMSO method was found to be more suitable for inclusion of genistein in dextran, resulting in a higher genistein load (5.6 ± 0.1 g genistein per 100 g particles), and a higher percentage of nanosized particles (85%, 105–400 nm). For both protocols, addition of a freeze-drying step exerted a positive effect presumably due to the formation of new hydrogen bonds and van der Waals interactions.