Agricultural production in regions such as sub-Saharan Africa (SSA) is very low as compared to other regions such as the Mediterranean area (MED). Differences are mainly due to agricultural input use which is generally lower in SSA. Indeed, in both regions, where unsustainable agricultural practices are largely applied although varying in intensification, soil organic carbon degradation and soil biodiversity decline are widespread issues. However, whether changes of soil microbial diversity have consequences on agroecosystem services, like crop productivity, in such agro-ecological zones is still scarcely investigated at field level.