Carbon dynamics in vegetated ecosystems are influenced by plants, belowground bacteria, and their interactions. Consequently, quantifying the fate of new plant production, identifying bacterial carbon sources, and evaluating plant–microbe interactions can provide insight to carbon cycling and storage. To follow short-term carbon transformations in a Spartinaalterniflora—soil system, we applied 13C-labeled CO2 to aboveground leaves and chased it belowground into roots and bacterial lipids. Plant mesocosms were exposed to 13CO2 for 0, 1, 3, or 6 h. Incorporation of 13CO2 by plants and soil microbes was measured immediately after the incubation (Day 0) and 24 h later (Day 1). During a 24 h period, 41–64 % of the 13CO2 fixed by S. alterniflora was retained in leaves, 2.7–6.4 % was transferred to roots, and 30–55 % was lost via respiration. Small fractions of 13C assimilated by aboveground leaves were detected belowground in bacterial lipids on Day 1. Enrichment of lipids specific to sulfate reducing bacteria (10-methyl C16:0, cy-C17:0) indicated tight coupling between aboveground plant production and belowground anaerobic metabolisms. Overall, we found that a substantial fraction of new production was returned to the atmosphere within 24 h and that belowground bacteria were tightly coupled to plant dynamics.