This work presents the development of a method for the synthesis of calcium silicate nanoparticles stabilized with essential amino acids. CaSiO3 nanoparticles were obtained through chemical precipitation. In the first stage, the optimal calcium-containing precursor was determined. The samples were examined using scanning electron microscopy. It was found that Ca(CH3COO)2 was the optimal calcium-containing precursor. Then, the phase composition of calcium silicate was studied using X-ray phase analysis. The results showed the presence of high-intensity bands in the diffractogram, which characterized the phase of the nanosized CaSiO3—wollastonite. In the next stage, the influence of the type of amino acid on the microstructure of calcium silicate was studied. The amnio acids studied were valine, L-leucine, L-isoleucine, L-methionine, L-threonine, L-lysine, L-phenylalanine, and L-tryptophan. The analysis of the SEM micrographs showed that the addition of amino acids did not significantly affect the morphology of the CaSiO3 samples. The surface of the CaSiO3 samples, both without a stabilizer and with amino acids, was represented by irregularly shaped aggregates consisting of nanoparticles with a diameter of 50–400 nm. Further, in order to determine the optimal amino acid to use to stabilize nanoparticles, computerized quantum chemical modeling was carried out. Analysis of the data obtained showed that the most energetically favorable interaction was the CaSiO3–L-methionine configuration, where the interaction occurs through the amino group of the amino acid; the energy value of which was −2058.497 kcal/mol. To confirm the simulation results, the samples were examined using IR spectroscopy. An analysis of the results showed that the interaction of calcium silicate with L-methionine occurs via the formation of a bond through the NH3+ group of the amino acid.