The development of microfluidics-based systems in the recent years has provided a rapid and controlled method for the generation of monodisperse microencapsulates for multiple applications. Here, we explore the design, manufacture and characterization of a low-cost microsystem for the encapsulation of the fungal laccase from Pycnoporus sanguineus CS43 in alginate microcapsules. Multiphysics simulations were used to overview the fluid behavior within the device and estimate the resulting capsule size. Polymethylmethacrylate (PMMA) sheets were used for final microsystem manufacture. Different flow rates of the continuous (Qc) and discrete (Qd) phases in the ranges of 83-293 mL/h and 1-5 mL/h, respectively, were evaluated for microcapsule fabrication. Universal Serial Bus (USB) microscope and image analysis was used to measure the final particle size. Laccase encapsulation was evaluated using spectrophotometry and with the aid of fluorescent dyes and confocal microscopy. Results showed microcapsule size was in the range of 203.13-716.00 μm and Qc was found as the dominant parameter to control capsule size. There was an effective enzyme encapsulation of 65.94% with respect to the initial laccase solution.