The calcium carbonate (CaCO3) cores being templates for model proteins encapsulation were obtained for developing oral drug delivery systems. The influence of the characteristics of the core formation (the time, the temperature, the stirring intensity, the ultrasound treatment and drying conditions) on the size and morphology of the carbonate cores was studied. The core size was shown to decrease with increasing the stirring time and stirring intensity. Statistical analysis of the scanning electron microscopy images of the carbonate cores allowed finding a correlation between their mean diameter and the parameters of the core formation. The regularities of proteins loading into porous CaCO3 cores were determined, and different loading methods were compared quantitatively. The co-precipitation method gives cores with the proteins load about five times as much as the adsorption method. The influence of protein properties and the ionic environment of protein molecules on the loading parameters were shown.