Hybrid materials based on calcium phosphates and synthetic polymers can potentially be used for caries protection due to their similarity to hard tissues in terms of composition, structure and a number of properties. This study is focused on the biomimetic synthesis of hybrid materials consisting of hydroxiapatite and the zwitterionic polymers polysulfobetaine (PSB) and polycarboxybetaine (PCB) using controlled media conditions with a constant pH of 8.0–8.2 and Ca/P = 1.67. The results show that pH control is a dominant factor in the crystal phase formation, so nano-crystalline hydroxyapatite with a Ca/P ratio of 1.63–1.71 was observed as the mineral phase in all the materials prepared. The final polymer content measured for the synthesized hybrid materials was 48–52%. The polymer type affects the final microstructure, and the mineral particle size is thinner and smaller in the synthesis performed using PCB than using PSB. The final intermolecular interaction of the nano-crystallized hydroxyapatite was demonstrated to be stronger with PCB than with PSB as shown by our IR and Raman spectroscopy analyses. The higher remineralization potential of the PCB-containing synthesized material was demonstrated by in vitro testing using artificial saliva.