Plant roots and soil biota interact with soil minerals and organic matter in a self-organized feedback system. Soil structure, as the habitat for soil organisms, exerts significant controls on their growth, activities, and turnover. Yet, through these processes soil organisms continually modify their habitat, altering the architecture of soil particles and pores and the stability of secondary aggregated structures. This feedback system similarly affects the cycling of soil organic matter. Hence, efforts to quantify soil organic matter transformations and dynamics are increasingly considering pools defined by their physical and temporal associations with soil structural components. Soil fractionation approaches that consider the interactions of soil organic matter and soil structure can be combined with isotopic tracers, molecular characterizations, and other advanced techniques and applied across temporal gradients to provide new insights to soil organic matter cycling and sequestration. Examples from chronosequence and repeated measure studies in grassland, shrubland, and forest systems will be presented. Interpretive considerations associated with the duration of tracer incorporation and system dynamics (i.e., aggrading, degrading, or steady-state systems) will be discussed.