The mosaic of soil microenvironments, that differ in physical, biological, and chemical properties, control the spatially and temporal variability of microbial mediated C and N cycling. Here, I summarize several studies investigating how soil C and N cycling is controlled by soil biotic activity and soil structural formation and degradation. It has been shown that soil microaggregate structures, and especially those included within macroaggregates, create an operationally definable habitat for microorganisms that is characterized by low predation pressure, relatively stable water potential, low O2 availability, and low accessibility for exogenous toxic elements. Indeed, amino sugar analyses have indicated that microbial-derived C is accumulated within microaggregates occluded within macroaggregates (mM), due primarily to a greater fungal-mediated improvement of soil structural stability and concurrent deposition of fungal-derived C. However, not only fungal activity leads to the formation of a stable soil structure, but also earthworms are know to actively form microaggregates within their casts and the bacterial population within these microaggregates is more stable than the population associated with macroaggregates. Recently, several studies have also shown that C is preferentially stabilized in microaggregates occluded within macroaggregates (mM) in soils under best management practices. In conclusion, best management practices should further capitalize on optimizing the feedback between soil structural formation, biotic activity and C and N cycling.