Stable intracellular symbiosis in Paramecium bursaria has been studied primarily in relation to its natural algal symbiont, zoochlorellae. In the present study, we examined the ultrastructural process by which yeast cells become established in aposymbiotic P. bursaria. Aposymbiotic cells, prepared by eliminating intracellular zoochlorellae, were experimentally infected with Pichia capsulata and Rhodotorula rubra. Light microscopy showed that both yeast species could be maintained within host cells for at least three months. Subsequent ultrastructural analysis by transmission electron microscopy (TEM) focused on intracellular P. capsulata. TEM revealed that intracellular P. capsulata was enclosed by a peri-symbiont vacuole membrane (PVM) and exhibited marked structural differences from its free-living counterparts. In free-living yeast, the cell wall was compact and densely organized, whereas in intracellular yeast, it was transformed into a loosened microfibrillar layer extending toward the PVM. These fibrils appeared to connect the yeast cell wall to the surrounding vacuolar membrane. During the early stage of infection, although some yeast cells were digested in food vacuoles, others retained their morphology, escaped from the vacuole while remaining membrane-enclosed, and ultimately localized in the cortical region near trichocysts. These observations indicate that intracellular establishment of yeast in P. bursaria involves partial resistance to digestion, escape from the food vacuoles, and stabilization within a membrane-bound compartment. Together, these findings suggest that yeast infection can serve as a valuable comparative model for understanding the structural basis of endosymbiosis in P. bursaria.