The preparation of microcapsules with a self-microemulsifying system (SMES) core using a vibrating nozzle technology was improved with regard to process reproducibility and core phase retention. The microcapsule shell was optimized for composition of the alginate-pectin (A/P) ratio and hydrophilic filling agent content. The best-shaped microcapsules with highest encapsulation efficiency for furosemide-loaded SMES were obtained from the shell-formation phase with an A/P ratio of 25:75, containing 10% lactose, which was hardened through a one-step process. Fluid bed-dried microcapsules were examined for their release characteristics and swelling behavior of the polymeric matrix. Incorporation of hydrophilic filling agents in the shell-formation phase was shown to be successful in limiting the leakage of the core phase during the microcapsule production and drying processes. Moreover, the addition of different fillers also allows the drug release profile from Ca-alginate/pectinate microcapsules with a self-microemulsifying core to be modified.