We used sporopollenin prepared from Lycopodium Clavatum to encapsulate living yeast cells as a model for probiotics. The microencapsulation of cells was achieved by using the trilite scars of the sporopollenin microcapsules which can open up by compressing the sporopollenin into a pellet. Such compressed pellets were exposed to an aqueous suspension of yeast cells in the presence of a biocompatible surface active agent which allowed living cells to be loaded inside the sporopollenin particles by the influx of liquid to the sporopollenin interior as the deformed microcapsules re-inflated to their original state. We demonstrated that the cells viability and biological activity is preserved after the microencapsulation in the sporopollenin. Such microencapsulation technology could find application in preserving cells from mechanical stress and aggressive environments which can be used in protection of probiotics in food formulations.