Reconstructed prairies can be a useful tool in combating climate change by acting as a sink for carbon (C) and nitrogen (N). However, little is known about where C and N gains occur in the soil matrix, and in turn whether they accumulate in pools characterized by relatively long or short mean residence time. To answer this question, a reconstructed prairie chronosequence spanning 21 years was used to observe changes in chemically and physically protected C and N pools. As these soils were finely textured, edaphic properties such as non-crystalline iron and polyvalent cations were also examined for associations with C and N pools. While there was a significant increase in both total soil C and N over time, pools chemically bound to silt/clay outside of microaggregates served as the largest stock in which new C and N was stabilized. Physically protected particulate organic matter did not increase with prairie age, but microaggregate silt/clay C and N concentrations were correlated with microaggregate ammonium oxalate extractable iron. These results contrast previously held understandings of microaggregate turnover under no-till soil environments such as reconstructed prairie. Future research must investigate why C and N stocks in reconstructed prairies are much less than remnants, and whether improved prairie management can affect physical or chemical protection of organic matter.