The membraneâprotein interface on lipidâbased nanoparticles influences their in vivo behavior. Better understanding may evolve current drug delivery methods toward effective targeted nanomedicine. Previously, the cellâselective accumulation of a liposome formulation in vivo is demonstrated, through the recognition of lipid phaseâseparation by triglyceride lipases. This exemplified how liposome morphology and composition can determine nanoparticleâprotein interactions. Here, the lipaseâinduced compositional and morphological changes of phaseâseparated liposomesâwhich bear a lipid droplet in their bilayerâ are investigated, and the mechanism upon which lipases recognize and bind to the particles is unravelled. The selective lipolytic degradation of the phaseâseparated lipid droplet is observed, while nanoparticle integrity remains intact. Next, the Tryptophanârich loop of the lipase is identified as the region with which the enzymes bind to the particles. This preferential binding is due to lipid packing defects induced on the liposome surface by phase separation. In parallel, the existing knowledge that phase separation leads to in vivo selectivity, is utilized to generate phaseâseparated mRNAâLNPs that target cellâsubsets in zebrafish embryos, with subsequent mRNA delivery and protein expression. Together, these findings can expand the current knowledge on selective nanoparticleâprotein communications and in vivo behavior, aspects that will assist to gain control of lipidâbased nanoparticles.