We examined relationships between the pore structure of microaggregates and the protection of organic matter (OM) within that structure. By using ultra-small angle X-ray scattering (USAXS) before and after combustion of microaggregates at 350°C, we took advantage of differences in X-ray scattering contrast among soil minerals, OM, and air to evaluate the distribution of the total- and OM-filled porosity within microaggregates (53–250μm in diameter). Systematic changes in microaggregate structure were observed for long-term field manipulations of land use (a chronosequence of tallgrass prairie restorations) and agricultural management (conventional tillage versus no-till at two levels of nitrogen fertilization). Our results imply that OM preservation arose from the evolution of the architectural system of microaggregates during their formation and stabilization. Soils and treatments with increasing OM in microaggregates were associated with encapsulation of colloidal OM by minerals, thereby creating protected OM-filled pores at the submicron scale within the microaggregate structure. For example, in the prairie chronosequence, microaggregates from the cultivated soil had the lowest concentration of OM, but 75% of the OM that had survived cultivation was in OM-filled pores. Following restoration, the concentration of OM in microaggregates increased rapidly, but the proportion of OM in OM-filled pores declined initially and then increased over time until 90% of the OM was in OM-filled pores. OM totally encapsulated within the pore structure can create spatial and kinetic constraints on microbial access to and degradation of OM. Encapsulation of OM increases the capacity for its protection relative to sorption on mineral surfaces, and comparison of its extent among treatments suggests important feedback loops. The use of USAXS, which has not previously been applied to the study of soil aggregate structures and the distribution of OM within those structures, provided new information on the mechanisms of OM protection in soil microaggregates, and insights relevant to strategies for enhancing carbon-sequestration in soil through changes in agricultural management practices and land use.