Abstract Encapsulated human retinal pigment epithelial cell line ARPE-19 has been successfully used in experimental cell therapy of retinal degenerations and Parkinson’s disease, but the long-term storage of encapsulated cells is still an unresolved question. Reconstitution of viable encapsulated cells from dry form would benefit the development of cell therapy products. We freeze dried and reconstituted microencapsulated ARPE19 and ARPE19-SEAP cells. Cross-linked alginate matrix with polycation (poly-l-lysine, cationic starch) coating was used for microencapsulation. Cell viability was assessed with fluorescence microscopy and oxygen consumption of the cells. Freeze dried and reconstituted cell microcapsules were imaged using scanning electron microscopy (SEM) and environmental scanning electron microscopy (ESEM). We show partial viability of microencapsulated cells after freeze-drying. Unlike poly-l-lysine (PLL) coating, cationic starch supported microcapsule shape and cell viability during freeze-drying. Trehalose pre-treatment augmented cell viability. Likewise, some lyoprotectants (trehalose, glycerol) enabled preservation of cell viability. Upon reconstitution the freeze dried cell microcapsules rapidly regained their original spherical shape. This proof-of-concept study demonstrates that microencapsulated cells can retain their viability during freeze-drying. Therefore, this approach can be further optimized for the benefit of cell therapy product development.