Within the Biodiversity Genomics Europe project, the "Ecological Restoration - Soil" case study was designed to evaluate changes in soil biodiversity during the process of ecological succession, sampling a chronosequence of replicated plots at different stages of restoration since land abandonment. The present SOP describes soil sampling under sterile and cold conditions for metabarcoding analyses. This case study involved sampling four successional stages, represented by specific vegetation types present in early (recently abandoned land) to old (mature forests) systems, including two intermediate recovery stages. The "Biodiversity Genomics Europe | Ecological Restoration - Soil” case study intends establishing a baseline for soil’s microbiome, fungi and arthropods diversity; to further monitoring, as well as to inform land usage strategies under farming practices, restoration and preservation of more conserved, successional areas.