Given the importance of soil as a supplier of nutrients and water for different ecosystems, understanding soil health and quality is necessary for its preservation. Microorganisms, due to their high abundance and their relationship with the degradation of organic matter and biogeochemical cycles, have a rapid response to environmental changes and thus are a discriminating factor that can be used as bioindicators of soil health. However, 97% of microorganisms are unculturable, leaving a gap in their taxonomic and functional knowledge. The development of metagenomics has reduced this problem through the direct extraction of DNA from soil, allowing the characterization of such non-culturable microorganisms, this technique can be considered one of the most impactful in soil health, given that it allows for an exploration of the biodiversity, the community structure, and the potential functions of the microbial communities from distinct environments. In addition to this, metagenomics have had an impact in different areas such as "OneHealth" or EcoGenomics allowing the formation of international projects. The aim of this paper is to show how metagenomics can be used as a technique to assess soil quality and health through the taxonomic and functional identifi cation of the microorganisms present in the soil.