Problem All agricultural soils harbour microbiome, consisting of a high diversity of bacteria, archaea, fungi and protists. Together they provide ecosystem services which are crucial for sustainable agriculture and a healthy environment. Agricultural soil management may not deliberately impact microbial diversity function, however it may possibly trigger adverse effects, e.g. higher production of greenhouse gases, increased levels of soil-borne pathogens or inefficient use of fertilisers. Solution Microbiomes strongly respond to environmental changes and management practices such as tillage (till versus no-till) and fertilisation. This responsiveness can be used for stirring their activities. Farming systems should be managed to promote diverse microbiomes, thereby stabilizing microbial ecosystem services. Examples of adapted management schemes are described in recommendations. More knowledge on promoting beneficial microbiomes should be generated through research.