Soil organic matter (SOM) represents a key indicator for soil quality in respect to both agricultural and environmental functions. SOM determines soil water properties, buffer capacity, resilience under stresses, and sustainability in production. Sequestration of carbon in cropland soils offset ~21% of cropland emissions in 2008. It has been documented that agricultural practices could create great potential for prioritizing soil quality and organic carbon storage in soils. In addition to chemical adsorption and biochemical stabilization, physical encapsulation of SOM in fine-scale pores may provide a very large potential for carbon stocks, because a much greater volume of SOM can be enclosed within a given surface area of minerals than can be adsorbed onto their surfaces. This study deals with the effects of different agricultural practices, such as manure application, chemical fertilizers, residue return, and cover crop, on the quantity and distribution of SOM in nano-/micro-sized pores of soil microaggregates. Specifically, we evaluated the distribution of the total- and SOM-filled porosity within microaggregates by taking advantage of differences in x-ray scattering contrast between soil minerals, SOM, and air, which were measured using ultra-small angle x-ray scattering (USAXS) before and after combustion of microaggregates at 350°C. Results show that the SOM preservation arises from the evolution of the architectural system of microaggregates during their formation and stabilization. Land-use options (conversion of soils from long-term cultivation to perennial vegetation) and agricultural treatments (conventional versus conservative tillages at different levels of chemical fertilizer inputs) with increasing SOM in microaggregates are associated with encapsulation of colloidal SOM by minerals. Our water retention measurements show that the SOM encapsulation in <5 µm diameter pores increases water retention in microaggregates, while management practices that either increased or decreased the abundance of SOM-filled pore volume in the microaggregates promoted hysteresis of water retention characteristics due to changes in soil pore structure. The water retention data measured on intact and combusted microaggregates are consistent with the SOM encapsulation from USAXS measurements, indicating that pore filling of SOM could create spatial and kinetic constraints on water flow and microbial access to increase the physical protection of SOM in soil pores. Management practices (such as organic practices and less residue removal) have a great potential for facilitating the synergistic retention of water and organic carbon in soils.