Lipase cartridges are currently the mainstay of treatment to improve fat absorption related to pancreatic insufficiency (PI) in patients receiving enteral nutrition feedings. Enzyme immobilization is an essential prerequisite for designing lipase cartridges systems for efficient enzymatic fat hydrolysis. A microfluidic approach has been adopted to produce lipase (LIP) caged in hyperbranched polyglycerol microcapsules (HPGly). The resulting HPGly-LIP microcapsules are spherical and had an average diameter of 29 µm with monomodal size distribution. The optimum conditions determined by artificial neural networks were HPGly concentration of 10 wt.%, LIP loading of 20% (wt) and total flow rate in microfluidic cell of 1.0 mL/h. Under these conditions, the maximum capacity of the LIP that can be microencapsulated is around 85% with respect to the HPGly concentration of 10 wt.% and total flow rate in microfluidic cell of 1.0 mL/h. This resultant HPGly-LIP exhibited Michaelis–Menten coefficients of 1.138,14 mM (K m) and 0.49 U/mg (V max) showing higher activity compared to free LIP. Finally, the robust HPGly-LIP microcapsules showed excellent recyclability. The in vitro Analysis of the HPGly-LIP cytotoxicity showed that microcapsules had no cytotoxic effect to L929 fibroblasts cells and behaved very similar to the negative control. These features will be useful for the facile construction of biocatalytic systems with high efficiency, excellent recyclability and adequate biocompatibility for treatment of patients with PI receiving enteral nutrition feedings.