<p>Understanding the response of biofilms to climatic conditions and their effects on cultural heritage sites is crucial for developing effective conservation strategies. Previous studies have primarily focused on microbial community responses to environmental factors, and little is known about how climatic conditions influence biofilm-induced deterioration and protection. Here we analyzed genomic data from stone heritage sites in East and South Asia and found that biofilm roles shifted from causing deterioration to offering protection along the transition from temperate to tropical climates. This shift was likely regulated by climate-driven variations in functional genes associated with dissimilatory nitrate reduction (<i>napAB</i>, <i>narGHI</i>, <i>nrfAH</i>, and <i>nirBD</i>) and assimilatory sulfate reduction (<i>cysJI</i> and <i>sir</i>). The expression of genes related to these pathways inhibits the accumulation of soluble salts and biogenic acids, leading to protective effects. This study elucidates the dynamic role of microbes in cultural heritage conservation and lays the foundation for sustainable preservation strategies.</p>