Electrostatic interaction plays a leading role in nanoparticle interactions with membrane architectures and can lead to effects such as nanoparticle binding and membrane disruption. In this work, the effects of nanoparticles (NPs) interacting with mixed lipid systems were investigated, indicating an ability to tune both NP binding to membranes and membrane disruption. Lipid membrane assemblies (LBAs) were created using a combination of charged, neutral, and gel-phase lipids. Depending on the lipid composition, nanostructured networks could be observed using in situ atomic force microscopy representing an asymmetrical distribution of lipids that rendered varying effects on NP interaction and membrane disruption that were domain-specific. LBA charge could be localized to fluidic domains that were selectively disrupted when interacting with negatively charged Au nanoparticles or quantum dots. Disruption was observed to be related to the charge density of the membrane, with a maximum amount of disruption occurring at similar to 40% positively charged lipid membrane concentration. Conversely, particle deposition was determined to begin at charged lipid concentrations greater than 40% and increased with charge density. The results demonstrate that the modulation of NP and membrane charge distribution can play a pivitol role in determining NP-induced membrane disruption and NP surface assembly.