Nanoparticles (NPs) with antimicrobial properties recently have emerged as an interesting study area. Different types of inorganic NPs (metal, oxide, alloy and mixture) have been synthesized and studied against Gram-positive and Gram-negative bacteria. Factors associated with the antimicrobial activity of NPs can be associated with the microorganism (e.g., bacterial cell wall, biofilm formation, etc) and with NPs (e.g., size, shape, chemical compositions). Here, we reviewed recent advances in relation with the interaction mechanisms of inorganic NPs with biomolecular systems of microorganism's cells. In particular, we analyzed the action mechanisms of AgNPs and the interaction of NPs with specific cell components. Factors associated with the antimicrobial activity of NPs can be associated with the microorganism (e.g., bacterial cell wall, biofilm formation, etc) and with NPs (e.g., size, shape, chemical compositions). NP can modify the secondary, tertiary and quaternary structures of polymer biomolecules as proteins and therefore its biological function can be affected. Results suggest that an initial point to understand the interaction of bacterial biomolecules with inorganic NPs is the nature of NPs (bulk and surface composition). Keywords: Antimicrobial activity, biomolecules, inorganic nanoparticle, lipid bilayer, nucleic acids, proteins.