Method of time-resolved micro-potentiometry was introduced for probing the kinetics of proton uptake by dormant Bacillus subtilis spores. It was shown that the plurality of steps comprising the uptake of protons may be attributed to the multi-layered structure of the spores. Based on the diffusion time analysis, it was found that the effective diffusion coefficient for hydrogen ions within the spore core can be up to 3 orders of magnitude lower than that within the coats and cortex. Estimated from the coupled proton diffusion and binding model, the concentrations of binding sites inside the spore layers appeared to be comparable with the spore proton capacity found from the equilibrium binding. Together with the known facts of the low level of water content (25-55% of the mass of the hydrated spore core), the bound state of water, the high level of dipicolinic acid (5-15% of the mass of the hydrated spore core) in the spore core, the immobility of a soluble protein in dormant spores, and the inner membrane lipids immobility, the high concentration of ionizable groups found in this work supposes that the spore cytoplasm is a particular state of biological matter characterized by a high density of charge within the nanosized matrix of the spore core. In the practical point of view, regulation of the spore internal pH may be the way of its metabolic dormancy control, since the internal pH may be a contributing factor to enzymatic activity within the dormant spore.