Ellagic acid (EA), a naturally occurring bioactive phenolic compound largely found in pomegranate, exhibits significant health benefits due to its antioxidant, antimutagenic, and even anticancerogenic properties. The present work aimed to microencapsulate EA extracted from pomegranate peels. To improve the stability of EA, microencapsulation was applied with Spirulina as a coating material. For this purpose, ethanolic extracts obtained from pomegranate peels were used for microencapsulation. Response surface methodology combined with a three-level, three-variable Box-Behnken design (BBD) was applied to obtain optimum microencapsulation. The microparticles obtained under the optimized encapsulation conditions were further characterized by FT-IR and SEM. The results confirmed the encapsulation of EA in Spirulina cells. Then, the optimum microparticles were used in an in vitro release study. The results of the in vitro digestion with simulated gastrointestinal fluids could help to determine the content and biological activity of EA. In this study, the effect of encapsulation on the release properties of EA during simulated gastrointestinal digestion was also evaluated. HPLC-DAD analysis and the Folin-Ciocalteu and ABTS methods were helpful for characterization of EA in the simulated fluids. The release profile of EA indicated that in simulated intestinal fluid, the release was faster than that in gastric fluid.