Microcapsules created by the layer-by-layer (LbL) polyelectrolyte adsorption technique have been sub-compartmentalised by embedding cubic mesophase lipid nanoparticles (cubosomes?) into the capsule shell wall. Monoolein and phytantriol cubosomes? containing fluorescent lipid and/or positively charged surfactant were first analysed for stability via dynamic light scattering, microelectrophoresis, and small angle X-ray scattering techniques. Once nanoparticle stability was confirmed, cubosomes? were embedded within a multilayer assembly of oppositely charged polyelectrolytes [poly(allylamine hydrochloride) and poly(styrene sulfonate)] on planar silica substrates. Deposition of each layer was monitored using a quartz crystal microbalance with dissipation monitoring. These findings were then correlated to the growth of polyelectrolyte films incorporating cubosomes? onto silica microparticles, where ?-potential measurements were used to monitor the deposition of each subsequent layer. Small angle X-ray scattering experiments provided verification that cubosomes? remained structurally intact when embedded within the polyelectrolyte matrix. Upon removal of the silica core, stable microcapsules containing one layer of embedded cubic nanoparticles were obtained. A diversity of molecular encapsulation matrices is offered through the capsule core, polyelectrolyte layers, and the embedded cubosomes? of these sub-compartmentalised, nanostructured microcapsules.