Covalent organic frameworks (COFs) have emerged as an important material for antimicrobial applications due to their customizable porous structures, abundant active sites, and good stability. In this perspective, we explore the topological connectivity in the construction of currently developed antimicrobial COFs, which mainly include –B–O–, –N–H–, β-ketoenamine, and azine/triazine. The advantages of pristine COFs in mono- and synergistic antimicrobials are integrated and discussed. We further summarize COF-embedded hybrid materials, such as COFs/metal nanoparticles, COFs/metal-organic frameworks, COFs/carbon materials, and COFs/other materials, and demonstrate the diverse material design and application concepts. Finally, we outline the challenges and promising prospects of COF materials in biomedical and industrial antimicrobial fields, emphasizing the need to explore these materials from a multidimensional perspective.