Herein, the polyelectrolyte capsules containing spectral and fluorescent probes were formed using the layer-by-layer method based on the layerwise deposition of oppositely charged polyelectrolytes on the micelles of different ionic surfactants, cetyltrimethylammonium bromide and sodium dodecyl sulfate, with previously solubilized substrates. The branched polyethyleneimine was used as a cationic polyelectrolyte, and the graft-copolymer with a polyimide backbone and polymethacrylic acid side chains acts as an anionic polyelectrolyte. The three-, five- and seven-layered capsules were synthesized. Dynamic light scattering method shows that irrespective of the nature of ionic surfactants the size of capsules ranges within 150–200 nm, but in the case of sodium dodecyl sulfate an increase the number of deposited layers results in an increase in particle size, whereas the opposite trend is observed in the case of cetyltrimethylammonium bromide. A charge of the surfactant used has little effect on the protective properties of the obtained capsules, but allows of forming the particles with different size behaviors, which can be important for the formation of nanocapsules and their use in drug delivery.