The association between the ciliate Paramecium bursaria and symbiotic Chlorella spp. is mutually beneficial. However, this relationship is facultative mutualism because both the host and the symbiotic algae can grow by themselves. This association is easily re-established by mixing the two species together. Following algal mixing, some algae become enclosed in the digestive vacuole membrane of the paramecia to which both acidosomes and lysosomes fuse. To establish endosymbiosis, some algae acquire temporal resistance to the host lysosomal enzymes in the digestive vacuoles. We examined whether the algae influence the differentiation of the host digestive process using LysoSensor staining to evaluate the acidification of the digestive vacuoles. Furthermore, to assess lysosomal fusion with the digestive vacuole, Gomori’s staining was conducted. Acidification and lysosomal fusion occurred later in digestive vacuoles containing living algae than in those containing boiled algae or latex spheres. This phenomenon was observed when the living algae were maintained under a constant light condition. These results suggest that the algae release some unknown factor in response to light exposure, and the factor may be associated with the alteration of the host digestive process, indicating that the living algae can influence the host digestive processes during early algal infection.