The weathering of building and sculptural stone due to increasing air pollution and salt damage results in the loss of invaluable cultural heritage artworks. This has prompted the design and application of novel and effective conservation treatments. Here, we study the effect of amorphous calcium carbonate (ACC) and oxalate (ACO) nanoparticles synthesized through an emulsion-assisted precipitation on alkoxysilane-based products, commonly used for the conservation of cultural heritage. Mimicking the mechanisms by which biominerals form via amorphous precursors and natural surfaces achieve high hydrophobicity through surface roughness (e.g., lotus leaf), alkoxysilane gels dosed with ACC and ACO nanoparticles were applied on different non-silicate substrates (marble, calcarenite, and gypsum). Our results show that this bioinspired approach for enhancing the performance of alkoxysilane-based treatments could be suitable for the protection of the aforementioned type of materials, as it has a limited aesthetic impact and negligible effects on hydric and water-vapor transport properties, while it foster compatibility with non-silicate surfaces, preventing drying crack development, enhancing resistance to acid attack, and increasing hydrophobicity due to nanoparticle-induced surface roughness. Best results were obtained using ACO nanoparticles.