The disclosure relates to novel microencapsulation processes based on the use of high viscosity fluids (e.g., gelatinized starch and alginate), which are mixed and then sprayed using a much gentler hydraulic pressure and, preferably gas-based atomization into a crosslinking solution (e.g. of calcium chloride). To improve the efficiency of the system, the process can be performed in a continuous mode rather than by a conventional batch process. This involves continuous or intermittent harvest of the microparticles collected in the capture vessel followed by amendment and recycling of the CaCl.sub.2 solution and its redeployment into the capture vessel. The process allows production of microencapsulated probiotic bacteria without major losses in viability, thereby providing a useful and efficient new manufacturing method for the stabilization of probiotic bacteria prior to their introduction into functional foods.