Phagocytic responses are critical for effective host defense against opportunistic fungal pathogens, such as Encephalitozoon cuniculi, an obligate intracellular fungus that causes emerging encephalitozoonosis in humans and other animals. Malassezia has immunomodulatory effects and can modulate the production of pro- and anti-inflammatory cytokines via keratinocytes and human monocytes. In this study, we evaluated the modulatory effects of heat-killed Malassezia pachydermatis suspension on macrophages challenged with Encephalitozoon cuniculi. Macrophages were treated with heat-killed M. pachydermatis suspension before being infected with spores of E. cuniculi. The cultures were stained with calcofluor, and the spores, internalized or not, were counted to determine their phagocytic capacity and index (PC and PI, respectively). Microbicidal and phagocytic activities were evaluated by transmission electron microscopy (TEM). The untreated macrophages had higher PC and PI and number of phagocytosed spores than treated macrophages. However, TEM revealed that treated macrophages had higher microbicidal activity because there were few spores in different degrees of degeneration and amorphous materials in the phagocytic vacuoles. Macrophages treated with heat-killed M. pachydermatis suspension had lower PC and PI and incipient presence of E. cuniculi in phagosomes. Treated macrophages had a mixed pattern of cytokine release with Th1, Th2, and Th17 profiles, with emphasis on interleukin (IL)-10, IL-4, IL-17, IL-6, and interferon (IFN)-γ secretion, and particularly high production of anti-inflammatory cytokines. Our results suggest that treatment with heat-killed M. pachydermatis suspension increases the release of cytokines and decreases the phagocytic activity of macrophages challenged with E. cuniculi.