Anti-fungal immunity is characterized by the continuous interplay between immune activation and immune regulation processes. These processes have now been clearly shown not only in animal pre-clinical models but also in humans. To create and maintain this immune homeostasis, reciprocal interactions among the host immune system, fungal pathogens, and the microbiome are crucial. Notably, the microbiome exerts multiple direct and indirect antifungal effects that are particularly aimed at minimizing host tissue damage. Thus, in this microbiome era, the architecture of 3D culture system or 'tissue organoids' might finally represent a simple but effective in vitro 'holobiont' to unravel the diverse interactions and adaptations that evolve to overcome fungal infections.