<p>The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus <i>Methanonatronarchaeum</i>, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.</p>