This review discusses relevant topics concerning the understanding of the characterization of antimicrobial coatings due to powerful antimicrobial nanoparticles in their composition. These coatings are utilized in the surface modification of yarns and materials designed for use in medical and dental applications. Various physical and chemical methods are employed to create these coatings, ensuring the development of efficient, homogeneous, and uniform layers on diverse surfaces and materials. The primary objective is to confer antimicrobial and/or antiviral properties upon these materials. For these coatings to be effective, they must incorporate active compounds that can combat a wide array of microorganisms, including those that have developed resistance to antibiotics. Examples of such active compounds include metallic nanoparticles such as silver, copper, and gold, as well as nanoparticles of metal oxides such as zinc, titanium, and aluminum. Upon the application of these coatings to medical materials, extensive testing and characterization procedures are undertaken, which will be thoroughly detailed in this review. It is crucial to emphasize that the absence of proper characterization and testing of nanoparticles in antimicrobial coatings could lead to the absence of standards, norms, or procedures necessary to safeguard human health and the environment. Despite their widespread application in the medical field, concerns have been raised regarding the potential toxicity of nanoparticles to living organisms. Consequently, this paper provides a comprehensive overview of the current state-of-the-art methodologies for characterizing nanoparticles in antimicrobial coatings, specifically focusing on materials with varying roughness and structures. Additionally, it outlines the issues associated with the potential accumulation of antimicrobial nanoparticles within the human body.