In this study, we explored the development of protective structural layers for stone cultural relics using biomineralization techniques. Our objective was to formulate protective materials with excellent acid resistance, stain resistance, and hydrophobic properties to serve as a functional material platform for sensing applications. The results showed that a protective layer with self-cleaning properties can be developed through biomineralization, effectively reducing the adhesion of contaminants. Quantitatively, the biomineralized coating exhibited superior performance, achieving contact angles as high as 149.28°, particularly on sandstone and basalt. Additionally, we included a comparative analysis with commercial materials. Experimental findings revealed that the protective coating developed in this study exhibits the highest drying speed and superior hydrophobicity. Importantly, the developed layer provides a stable interface that is compatible with integrated sensor systems for the long-term, smart monitoring of stone heritage degradation. Overall, the feasibility of using biomineralization techniques for protective coatings is high, showing significant potential for smart conservation in outdoor stone cultural relics.