The impact of soil microbial diversity on belowground forest processes, and effects on ecosystem functions in old-growth, managed and disturbed forests is poorly understood. We help stakeholders make decisions about the conservation of tomorrow’s forests by providing critical information on soil microbial diversity and belowground ecosystem services. We generate the best sampling and analytical practices on how soil environmental DNA (eDNA) can be used to map the presence of rare and red-listed species in ecosystems and assess the conservation value of forests. MicroEco establishes the impact of forest management on belowground taxonomic and functional diversity by comparing managed or disturbed forest ecosystems with relatively pristine, old-growth sites. State of the art tools from molecular biology (as probe-based capture) and biogeochemistry are used to understand the functioning of the soil ecosystem. Based on these, we will build models of ecosystem services. In particular, we will address the trade-offs and synergies of different services. Stakeholders will be engaged in our project through a series of workshops that aim to improve the conservation of the forests based on soil-based services.