The biodeterioration of the natural surface on monuments, historical buildings, and even public claddings brings to the attention of researchers and historians the issues of conservation and protection. Natural stones undergo changes in their appearance, being subjected to deterioration due to climatic variations and the destructive action of biological systems interfering with and living on them, leading to ongoing challenges in the protection of the exposed surfaces. Nanotechnology, through silver nanoparticles with strong antimicrobial effects, can provide solutions for protecting natural surfaces using specific coupling agents tailored to each substrate. In this work, surfaces of two common types of natural stone, frequently encountered in landscaping and finishing works, were modified using siloxane coupling agents with thiol groups. Through these agents, silver nanoparticles (AgNPs) were fixed, exhibiting distinct characteristics, and subjected to antimicrobial analysis. This study presents a comparative analysis of the efficiency of coupling agents that can be applied to a natural surface with porous structures, when combined with laboratory-obtained silver nanoparticles, in reducing the formation of microbial biofilms, which are a main trigger for stone biodeterioration.