The application of metagenomics uncovering stone-dwelling microbiotas and its functional capabilities are of great significance for early warning of stone monuments deterioration and screening of antimicrobial agents. Here, by harnessing the combination of Nanopore and Illumina sequencing, we investigated the microbial community compositions and potential risks resulting from elemental nitrogen (N) and sulfur (S) metabolism and environmental resistomes. Taxonomic profiling showed that lichenized Ascomycota and Actinobacteria dominate the microbial population in the biofilm, followed by Cyanobacteria, Proteobacteria, and Acidobacteria. Certain microbial groups and gene families were responsible for the biogeochemical N/S cycling, probably contributing to the succession and expansion of stone biodeterioration. High abundant and diverse antibacterial biocide and metal resistance genes were retrieved from assembled genome contigs, including those encoding resistance to copper (copR and copS), zinc (znuC/yebM and zraR/hydH), and quaternary ammonium compounds (gale and vcaM). Conversely, antibiotic resistance genes conferring resistance to multiple-antibiotic, aminoglycoside, and glycopeptide accounted for the relatively low percentage of total microbial metagenome. Binned genomes have further confirmed that bacterial species contained diverse antimicrobial resistance genes and mobile genetic elements, implying the possibility of horizontal gene transfer between bacterial lineages. Overall, our findings expand our knowledge of stone-dwelling microbiome and suggest appropriate treatment for stone biodeterioration.