We present a new method to incorporate hydrophilic charged nanoparticles into the lyotropic liquid crystal (LLC) template. This method is based on the effect of the polymer-induced phase separation (PIPS) and consists of two steps. In the first step, the nanoparticles are mixed with a surfactant micellar solution. In the second step, upon addition of polymer, phase separation is induced and the LLC phase doped with the nanoparticles is formed. Columnar hexagonal and lamellar LLC templates are obtained with the PIPS method. The ordering of the LLC phase can be controlled by the amount of polymer added to induce phase separation. The method works both for the system of nonionic surfactants and polymers and ionic surfactants and polyelectrolytes. We demonstrate that the PIPS method enables the fabrication of the LLC templates doped with positively or negatively charged nanoparticles as well as with a mixture of oppositely charged nanoparticles in arbitrary proportions.