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Soil quality is the capacity of a specific kind of soil to function, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, maintain or enhance water and air quality, and support human health and habitation. Soil organisms are assumed to be directly responsible for soil ecosystem processes, especially the decomposition of soil organic matter and the cycling of nutrients. Since soil quality is strongly influenced by microbe-mediated processes, and function can be related to diversity, it is likely that microbial community structure will have the potential to serve as an early indication of soil degradation or soil improvement. Here I tried to define the impact of different management practices on the fate of microbial guilds having fundamental role in soil healthiness and functions. Moreover, I attempted to manipulate experimentally soil microbial diversity to ask a central ecological question: is there a relationship between survival of exotic species and diversity? Answering this question would contribute to the debate on biodiversity and soil functioning, unfortunately still open after decades of theoretical and experimental works. Understanding of the microbial fate, and subsequent ecosystem functional modifications, are necessary to drive political decisions about the best practises to apply at the different territorial scales. The final goal is always improving soil quality and conservation practices.