There are many studies devoted to the application of polyelectrolyte microcapsules (PMC) in various fields; however, there are significantly fewer studies devoted to the study of the polyelectrolyte microcapsules themselves. The study examined the mutual arrangement of the polyelectrolytes in 13-layered PMC capsules composed of (PAH/PSS)6PAH. The research showed that different layers of the polyelectrolyte microcapsules dissociate equally, as in the case of 13-layered PMC capsules composed of (PAH/PSS)6PAH with a well-defined shell, and in the case of 7-layered PMC capsules composed of (PAH/PSS)3PAH, where the shell is absent. The study showed that polyallylamine layers labeled with FITC migrate to the periphery of the microcapsule regardless of the number of layers. This is due to an increase in osmotic pressure caused by the rapid flow of ions from the interior of the microcapsule into the surrounding solution. In addition, FITC-polyallylamine has a lower charge density and less interaction with polystyrene sulfonate in the structure of the microcapsule. Meanwhile, the hydrophilicity of FITC-polyallylamine does not change or decreases slightly. The results suggest that this effect promotes the migration of labeled polyallylamine to a more hydrophilic region of the microcapsule, towards its periphery.