A ¹³CO₂-labeling experiment was conducted in long-term conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato systems (Zea mays L.- Lycopersicum esculentum L.) to better understand the impact of cropping systems on microbial communities and C processing within soil microenvironments in the rhizosphere of a cover crop. New root-C from ¹³C-labeled hairy vetch (Vicia dasycarpa) plants were traced into phospholipid fatty acids (PLFA) within microaggregate (53-250 µm) and silt-and-clay (<53 µm) fractions in rhizosphere and non-rhizosphere soil.  In both microaggregates and silt-and-clay, total PLFA biomass and root-derived PLFA-C were approximately four and 10 times greater in the rhizosphere than in the non-rhizosphere, respectively.  Nevertheless, relative distributions of root-derived PLFA-C (¹³C mol%) in the rhizosphere- and non-rhizosphere were similar, thereby suggesting that the structure of the microbial community utilizing new root-C in the rhizosphere- and non-rhizosphere were not different.  Also, we did not find that one microbial group dominated the processing of new root-C (normalized for total C_new assimilation) in the microenvironments of the rhizosphere or non-rhizosphere. The composition of the microbial communities processing root-derived C were similar among the three cropping systems, which implied that the cropping systems maintained diverse microbial communities that are capable of utilizing various C substrates despite receiving different long-term nutrient inputs.  Results from principal component analyses suggested that the microbial community of the silt-and-clay in the rhizosphere played a different role in the cycling of new root-C compared to communities in the microaggregates and those in the silt-and-clay and microaggregates of non-rhizosphere soil. In light of the few studies on in situ root-C dynamics, our data illustrates the contribution of microbial communities to the stabilization of root-C in soil organic matter.