Long-term sustainability of soils with a prolonged history of crop production can be better understood by characterizing soil aggregation, particularly the distribution of carbon (C) and nitrogen (N) among particulate organic matter (POM) fractions within various soil aggregate-size fractions. The objective of this field study was to evaluate the effects of residue level, residue burning, tillage, and irrigation on macro-aggregate (>250 μm), micro-aggregate (53–250 μm), coarse (>250 μm) and fine POM (53–250 μm), and silt-clay fractions and their associated C and N in the top 10 cm of a highly erodible loessial soil (Glossaquic Fraglossudalf) after 13 years of consistent management in a wheat-soybean, double-crop (WSDC) system in the Lower Mississippi River Delta region of eastern Arkansas. The total aggregated soil fraction was 11.2% greater (P = 0.02) in the no-tillage (NT)-irrigated compared to the average of the other three tillage-irrigation combinations, which did not differ. Averaged over irrigation, burn, and residue-level treatments, the C concentration in the sand-free macro-aggregate fraction was 8.8% less (P < 0.05) under conventional tillage (15.6 g kg−1) than under NT (17.1 g kg−1). Fine POM C and N concentrations within sand-free-adjusted aggregates were 1.9 times greater (P ≤ 0.04) in the burn-low (2.59 and 0.21 g kg−1, respectively) compared to the burn-high treatment (1.35 and 0.11 g kg−1, respectively), while that in the no-burn under either residue level, which did not differ, were intermediate (2.43 and 0.23 g kg−1, respectively). Results showed that alternative management practices, such as NT and non-burning, can contribute to improved soil health and long-term sustainability and the mitigation of climate-change-related greenhouse gas concentrations in the atmosphere by reducing SOM oxidation, microbial respiration, and carbon dioxide emissions.