The goal of this work was the development of magnetic cross link enzyme aggregates (mCLEAs) of rhamno-pyranosidase (Rhmnase), prepared by chemical cross-linking with functionalized magnetite nanoparticles for glycompounds biosynthesis in microbioreactors (specially design 24-well microplate and mini-packed bed). Rhamnopyranosidase (EC number 3.2.1.40) present high potential in glycocompounds production, with applications in food and pharmaceutical industries. The influence of precipitants, cross-linkers, temperature and time on (m) CLEAs@Rhmnase development were optimized. Biocatalyst activity was accessed in the hydrolysis of 4', 5,7-trihydroxyflavanone-7-rhamnoglucoside and kinetic constants in the deglycosylation reaction were evaluated. Rhmnase operational stability was enhanced in mCLEAs, retaining almost 90% initial activity after 7 cycles of 24 h each. In a mini-packed bed bioreactor a maximum volumetric productivity of 140 mu mol/L. h was attained. In this bioreactor the operational stability of mCLEAs@Rhmnase were evaluated at a flow rate of 5 mL/h during 5 days and a residual activity of 95% was observed.