Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called "sediments" here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated withProteobacteria,Acidobacteria,Actinobacteria, andBacteroidetesat the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple.