In this study, we sought to link short-term cover crop-C and N cycling to microbial communities within soil organic matter (SOM) microenvironments. We collected soil samples (0-15cm) from long-term organic, low-input, and conventional maize-tomato rotations (Davis, CA), across the post-cover-crop maize growing season. Three SOM microenvironments were isolated from the soil samples: coarse particulate organic matter (CPOM; >250µm), microaggregates (53-250µm), and silt-and-clay (<53µm). We hypothesized that cover crop-C and -N inputs promote soil aggregation and stimulate microbial cycling of C and N within the microaggregates, by increasing the abundance of denitrifiers and ammonia oxidizing bacteria (AOB) in this fraction, particularly in the organic cropping system. Quantitative polymerase chain reactions (qPCR) using primers for the functional genes, amo A and nos Z, were employed to quantify AOB and denitrifier population sizes, respectively, in the microenvironments. To link cover crop-C cycling to the C-transforming microbial community, 13C-phospholipid fatty acid assays were also completed. Although few differences were found in the community fingerprints and bacterial abundances across the three cropping systems, the copy numbers g-1 dry soil of amo A and nos Z were highest in the microaggregate fraction and similar between the CPOM and silt-and-clay fractions. The lack of differences in the microbial community structure and activity across the three cropping systems does not explain the disparate C and N stabilization trends observed at the field-scale (organic: 5.70 Mg SOC ha-1 versus conventional and low-input: ~115 kg SOC ha-1), after 13 years of continuous cropping management; however, the differences in the 13C-labeled biomarkers and the populations of nitrifiers and denitrifiers at the microenvironment-level provide insight into mechanisms governing short-term C and N stabilization. Moreover, these results corroborate our hypothesis that the microaggregate is a unique microenvironment, where microbial processing of C and N is enhanced.