The nanoprecipitation of hydrogel nanoparticles by complex coacervation is investigated through a systematic study of the popular chitosan-polyphosphate pair of polyelectrolytes with opposite charges at pH 4. Polyphosphates of varying molar masses and electrical charges are investigated as alternatives to the commonly used tripolyphosphate, so as to assess the influence of the strength of electrostatic interactions on the fabrication possibility, the size of hydrogel particles, and their overall charge. Sodium hexametaphosphate and sodium polyphosphate allow the manufacture of such nanoparticles with either a positive or a negative charge, depending on the chitosan/polyphosphate ratio and the order of mixing. The classical way of mixing by pouring the polyphosphate solution into the chitosan solution yields microparticles. Inverting the order of mixing by pouring the chitosan solution into the polyphosphate solution allows the precipitation of negatively charged nanoparticles with diameters in the range 100-200 nm. Such charge inversion of the chitosan into negative is not possible with the common TPP. It was achieved using sodium hexametaphosphate and sodium polyphosphate having a larger negative charge. Charge inversion of chitosan allows an efficient encapsulation of positively charged proteins with an improved encapsulation efficiency than in the usual TPP-based coacervate. The encapsulation of the bovine serum albumin at pH 4 is given as a case study of a positively charged protein.