Soil processes are significantly regulated by biological activities. Soil ecosystem engineers (predominantly termites, earthworms and ants) and roots produce biogenic structures, aggregates or pores that determine the structure and architecture of soil. The sum of structures produced by a population or community of invertebrate engineers creates a specific environment defined here as a functional domain. Functional domains are characterized by (i) the nature and spatial array of the biogenic structures, solid aggregates, mounds or constructs and pores of different shapes or sizes; (ii) the specific communities of smaller organisms from the meso- and microfauna and micro-organisms that they host; and (iii) the spatial and temporal scales at which soil processes operate. The regulation of processes caused by the physical organization of the soil environment and the redistribution of organic resources have been described and quantified in several studies. In soil, the relative importance of regulation imposed by ecosystem engineering is likely to be greater than regulation by trophic relationships because of the specific ecological constraints observed in this environment when compared to above-ground conditions.