High-porosity stones in built heritage are vulnerable to damage mechanisms that compromise their integrity and cultural value. A multilayer treatment combining consolidation and protection can mitigate existing damage and reduce susceptibility to future deterioration. However, a critical factor in the success of conservation treatments is their compatibility with the material, i.e., their ability to avoid causing negative changes. This paper analyzes three key indicators of incompatibility for a multilayer conservation treatment applied to two historic Portuguese stones: Ançã Stone (limestone) and Silves Sandstone. The multilayer treatment involved ethyl silicate consolidation followed by a superficial protective layer. While color alterations were less noticeable on Ançã Stone, the negative changes in water vapor permeability and drying rates were significantly smaller in Silves Sandstone. Its larger porosity resulted in the alterations to its porous microstructure having a less significant impact on its water transport behavior. Interestingly, most of the observed changes are attributed to the consolidation treatment, as the protective layer did not introduce additional risks for either stone. Overall, the multilayer treatment posed a lower risk to Silves Sandstone compared to Ançã Stone, reducing the likelihood of accelerating damaging processes and demonstrating better conservation potential.