The main purpose of this work is to provide a comprehensive overview on the preparation of multifunctional epoxies, with improved antimicrobial activity and enhanced mechanical properties through nanomodification. In the first section, we focus on the approaches to achieve antimicrobial activity, as well as on the methods used to evaluate their efficacy against bacteria and fungi. Relevant application examples are also discussed, with particular reference to antifouling and anticorrosion coatings for marine environments, dental applications, antimicrobial fibers and fabrics, and others. Subsequently, we discuss the mechanical behaviors of nanomodified epoxies with improved antimicrobial properties, analyzing the typical damage mechanisms leading to the significant toughening effect of nanomodification. Some examples of mechanical properties of nanomodified polymers are provided. Eventually, the possibility of achieving, at the same time, antimicrobial and mechanical improvement capabilities by nanomodification with nanoclay is discussed, with reference to both nanomodified epoxies and glass/epoxy composite laminates. According to the literature, a nanomodified epoxy can successfully exhibit antibacterial properties, while increasing its fracture toughness, even though its tensile strength may decrease. As for laminates—obtaining antibacterial properties is not followed by improved interlaminar properties.