Stone consolidants have been widely used to protect historical monuments. Consolidants and hydrophobic formulations based on the use of tetraethoxysilane (TEOS) and alkylalkoxysilanes as precursors have been widely applied, despite their lack of solubility in water and requirement to be applied in organic media. In the search for a “greener” alternative based on silicon that has potential use in this field, the use of tetrakis(2-hydroxyethyl)silane (THEOS) and tris(2-hydroxyethyl)methyl silane (MeTHEOS) as precursors, due their high water solubility and stability, is proposed in this paper. It is already known that THEOS and MeTHEOS possess remarkable compatibility with different natural polysaccharides. The investigated approach uses the water-soluble silanes THEOS–chitosan and MeTHEOS–chitosan as a basis for obtaining hybrid consolidants and hydrophobic formulations for the conservation of siliceous and calcareous stones. In the case of calcareous systems, their incompatibility with alkoxysilanes is known and is expected to be solved by the developed hybrid consolidant. Their application in the conservation of building stones from historical and archeological sites from Guanajuato, México was studied. The evaluation of the consolidant and hydrophobic formulation treatment was mainly conducted by determining the mechanical properties and contact angle measurements with satisfactory results in terms of the performance and compatibility with the studied stones.