Polymer-stabilized perylene nanoparticles were prepared through a solvent exchange method. The formation of the nanostructures in aqueous solution was confirmed by the appearance of a red-shifted emission attributable to the formation of excimer-like aggregates. The behavior of organic nanostructures in the presence of lipid vesicles was investigated through steady-state and time-resolved fluorescence measurements. When no further surface treatment is applied to the nanoparticles, changes in the decay times and emission spectra demonstrate that inside the lipid bilayers the nanoparticles redissolve into the monomeric form with a rate and efficiency determined by the working temperature (above and below the transition temperature Tm of the phospholipid). On the other hand, when the stabilized shell is UV-cured to induce photo-cross-linking of the polymeric chains, the nanoparticle stability increases and their redissolution in the membrane is prevented. Confocal fluorescence images support the data obtained in bulk. The results indicate that the prepared nanostructures could be successfully used either as nanometric carriers for the delivery of poor water-soluble lipophilic compounds or as imaging tools depending on the rigidity/cross-linking degree of their polymeric stabilizer shell.