Microbes, commensals and pathogens, control numerous functions in host cells. They can alter host signaling and modulate immune surveillance by interacting with host proteins. To shed light on the contribution of microbes to health and disease, it is vital to discern how microbial proteins rewire host signaling and through which host proteins. Host-Microbe Interaction PREDictor (HMI-PRED) is a user-friendly web server for structural prediction of protein-protein interactions (PPIs) between host and a microbial species, including bacteria, viruses, fungi, and protozoa. HMI-PRED relies on "interface mimicry" through which the microbial proteins hijack host binding surfaces. Given the structure of a microbial protein of interest, HMI-PRED will return structural models of potential host-microbe interaction (HMI) complexes, the list of host endogenous and exogenous PPIs that can be disrupted, and tissue expression of the microbe-targeted host proteins. The server also allows users to upload homology models of microbial proteins. Broadly, it aims at large-scale efficient identification of HMIs. The prediction results are stored in a repository for community access. HMI-PRED is free and available at https://interactome.ku.edu.tr/hmi.