Although agrifood systems are heavily reliant on nitrogen inputs, most crops (and especially cereals) have low nitrogen utilization efficiency (30–50%). This means that much of the nitrogen applied in agroecosystems ends up in the atmosphere or terrestrial and aquatic ecosystems, which then causes the nitrogen cycle to spiral out of control, in turn leading to various problems such as eutrophication and higher nitrous oxide emissions. This nitrogen cycle is largely governed by soil microorganisms. Recent research, supported by the European Commission, has explored new strategies for more sustainable soil nitrogen management (e.g. improving nitrogen retention in agricultural systems), with the development of solutions and levers for action based on microbiota management (Theme 3 of the HOLOFLUX metaprogramme). The current scientific approach to microbial management is basically to inoculate microbial strains or consortia to make limiting nutrients bioavailable, or to implement biological control. But many questions remain about the sustainable deployment of these inoculants, and specifically their persistence, their non-target effects and the proliferation of potential invasive microorganisms.