In this study, a novel strategy has been developed for the assembly of polyelectrolyte multilayer (PEM) on CaCO3 templates in acidic pH solutions, where consecutive polyelectrolyte layers (heparin/poly(allylamine hydrochloride) or heparin/chitosan) were deposited on PEM hollow microcapsules established previously on CaCO3 templates. The PEM build-up, hollow capsule characterization and successful encapsulation of fluorescein 5(6)-isothiocyanate (FITC)-Dextran by coprecipitation with CaCO3 are demonstrated. Improvement by the removal of CaCO3 core was achieved while the depositions. In the course of the release profile, high retardation for encapsulated FITC-Dextran was observed. The combined shell capsules system is a significant trait that has potential use in tailoring functional layer-by-layer capsules as intelligent drug delivery vehicles where the preliminary in vitro tests showed the responsiveness on the enzymes.