The sol-gel process is a wet chemical technique that allows very fine control of the composition, microstructure, and final textural properties of materials, and has great potential for the synthesis of endodontic cements with improved properties. In this work, the influence of different sol-gel synthesis variables on the preparation of endodontic cement based on calcium silicate with Ca/Si stoichiometry equal to 3 was studied. Starting from the most optimal hydraulic composition selected, a novel second post-synthesis treatment using ethanol was essayed. The effects of the tested variables were analyzed by X-ray diffraction, infrared spectroscopy, scanning electron microscopy, nitrogen physisorption, and Gillmore needles to determine the setting time and simulated body fluid (SBF) immersion to measure the bioactive response in vitro. The results indicated that the sol-gel technique is effective in obtaining bioactive endodontic cements (BECs) with high content of the hydraulic compound tricalcium silicate (C3S) in its triclinic polymorph. The implementation of a novel post-synthesis treatment at room temperature using ethanol allows obtaining a final BEC product with a finer particle size and a higher CaCO content, which results in an improved material in terms of setting time and bioactive response.