Increasing soil organic carbon (SOC) stocks in agricultural soils can contribute to stabilizing or even lowering atmospheric greenhouse gas (GHG) concentrations. Cover crop rotation has been shown to increase SOC and provide productivity benefits for agriculture. Here we used a split field design to evaluate the short-term effect of cover crop on SOC distribution and chemistry using a combination of bulk, isotopic, and spectroscopic analyses of size-and density-separated soil aggregates. Macroaggregates (>250 µm) incorporated additional plant material with cover crop as evidenced by more negative δ¹³C values (−25.4‰ with cover crop compared to −25.1‰ without cover crop) and increased phenolic (plant-like) resonance in carbon NEXAFS spectra. Iron EXAFS data showed that the Fe pool was composed of 17–21% Fe oxide with the remainder a mix of primary and secondary minerals. Comparison of oxalate and dithionite extractions suggests that cover crop may also increase Fe oxide crystallinity, especially in the dense (>2.4 g cm⁻³) soil fraction. Cover crop δ¹³C values were more negative across density fractions of bulk soil, indicating the presence of less processed organic carbon. Although no significant difference was observed in bulk SOC on a mass per mass basis between cover and no cover crop fields after one season, isotopic and spectroscopic data reveal enhanced carbon movement between aggregates in cover crop soil.