The hexagonal CoO2 layer is an integral part of many important functional materials such as the LixCoO2 battery electrode, the NaxCoO2 and [CoCa2O3]0.62CoO2 thermoelectrics, and the Na0.3CoO2(H2O)1.3 superconductor. However, the CoO2-layer piling is prone to incorporate not only positively-charged metal and metal oxide layers but also protons between successive CoO2 layers. Here we systematically investigate the de-intercalation of the intervening alkali metal and metal oxide layers, and the subsequent intercalation of protons for an extensive series of LiCoO2, NaxCoO2 (x = 0.6–0.9) and [CoCa2O3]0.62CoO2 samples. First, we demonstrate the partial extraction of sodium from NaxCoO2 through immersion in an aqueous solution of either n-butylamine or NH4NO3. Such a treatment results in an appreciably low Na content of x = 0.37 or 0.10, respectively, but a simultaneous incorporation of certain amounts of charge balancing protons into the crystal lattice. Then, using a newly developed hydrothermal route we demonstrate the complete de-intercalation of the alkali and alkaline earth metal species from LiCoO2, NaxCoO2 and [CoCa2O3]0.62CoO2, and the intercalation of protons between the CoO2 layers. Finally we synthesize and characterize a water-containing NaxCoO2(H2O)z sample for comparison. As the protonation is found to be a common tendency of all the studied multilayered functional materials based on the CoO2 layer we believe that our work is not only of fundamental scientific interest but also of more practical relevance.