Nanotoxicity studies have shown that both carbon-based and inorganic engineered nanoparticles can be toxic to microorganisms. Although the pathways for cytotoxicity are diverse and dependent upon the nature of the engineered nanoparticle and the chemical environment, numerous studies have provided evidence that direct contact between nanoparticles and bacterial cell membranes is necessary for cell inactivation or damage, and may in fact be a primary mechanism for cytotoxicity. The propensities for nanoparticles to attach to and disrupt cell membranes are still not well understood due to the heterogeneous and dynamic nature of biological membranes. Model biological membranes can be employed for systematic investigations of nanoparticle-membrane interactions. In this article, current and emerging experimental approaches to identify the key parameters that control the attachment of ENPs on model membranes and the disruption of membranes by ENPs will be discussed. This critical information will help enable the "safe-by-design" production of engineered nanoparticles that are nontoxic or biocompatible, and also allow for the design of antimicrobial nanoparticles for environmental and biomedical applications.