HypothesisThe internal organization of polyelectrolyte layers deposited on colloidal templates plays a very important role for the potential applications of these systems as capsules for drug delivery purposes. ExperimentsThe mutual arrangement of oppositely charged polyelectrolyte layers upon their deposition on positively charged liposomes has been studied by combining up three different scattering techniques and Electronic Spin Resonance, which has provided information about the inter-layer interactions and their effect on the final structure of the capsules. FindingsThe sequential deposition of oppositely charged polyelectrolytes on the external leaflet of positively charged liposomes allows modulating the organization of the obtained supramolecular structures, impacting the packing and rigidity of the obtained capsules due to the change of the ionic cross-linking of the multi-layered film as a result of the specific charge of the last deposited layer. The possibility to modulate the properties of the LbL capsules by tuning the characteristics of the last deposited layers offers a very interesting route for the design of materials for encapsulation purposes with their properties controlled almost at will by changing the number of deposited layers and their chemistry.