In the past 20 years, AIEgens-based applications have been extensively developed, especially in biomedical field, including biosensing, bioimaging, cancer theranostics, microbe inactivation, and so on. This review aims to highlight the latest advances of AIEgens-based biomaterials for theranostics of bacteria, fungi and viruses. Based on the nature of these three pathogens, AIEgens are well modified and thus endowed with the capability of pathogen differentiation and selective imaging. Integrated with chemotherapeutic activity or phototherapeutic activity, multifunctional AIE biomaterials are developed for efficient pathogen inactivation.