Swift developments in nanotechnology have prominently encouraged innovative discoveries across many fields. Carbon-based nanomaterials have emerged as promising platforms for a broad range of applications due to their unique mechanical, electronic, and biological properties. Carbon nanostructures (CNSs) such as fullerene, carbon nanotubes (CNTs), graphene and diamond-like carbon (DLC) have been demonstrated to have potent broad-spectrum antibacterial activities toward pathogens. In order to ensure the safe and effective integration of these structures as antibacterial agents into biomaterials, the specific mechanisms that govern the antibacterial activity of CNSs need to be understood, yet it is challenging to decouple individual and synergistic contributions of physical, chemical and electrical effects of CNSs on cells. In this article, recent progress in this area is reviewed, with a focus on the interaction between different families of carbon nanostructures and microorganisms to evaluate their bactericidal performance.