Soil is one of the most diverse ecosystems on the planet, with a community of interacting bacteria, archaea, viruses, fungi, and protozoa collectively referred to as the "soil microbiome". These microorganisms play a crucial role in nutrient cycling, pathogen regulation, and soil carbon sequestration, and have direct and indirect effects on the health of plants and animals in terrestrial ecosystems. Biodiversity characterization has been widely used to reliably monitor and assess the state of the environment. In the last decade, the use of high-throughput sequencing has substantially advanced our understanding of the biogeography and ecology of soil bacterial and fungal communities worldwide. However, a recent review of global publications on soil biodiversity shows that Latin America contributes only 4% of the total information, whereas 87% of soil biodiversity research comes from the Northern Hemisphere. In the present study, samples of soils used for coffee cultivation were collected from 3 geographical zones located in Colombia: Quinchia (Risaralda), El Tambo (Cauca), and Minca (Magdalena) during the year 2021. The samples were processed for DNA extraction (LIMMA Laboratory - Universidad de Los Andes, Colombia) and sequenced (INTA Argentina) to obtain the final sequences. The raw sequences were loaded into ENA/MGnify with free access and subsequently subjected to taxonomic and diversity analysis for bacteria and fungi. This research was funded by the UKRI-BBSRC "Capacity building for bioinformatics in Latin America" (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1].