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A longstanding puzzle in isotope studies of C-3 plant species is that heterotrophic plant organs (e.g., stems, roots, seeds, and fruits) tend to be enriched in C-13 compared to the autotrophic organ (leaves) that provides them with photosynthate. Our inability to explain this puzzle suggests key deficiencies in understanding post-photosynthetic metabolic processes. It also limits the effectiveness of applications of stable carbon isotope analyses in a variety of scientific disciplines ranging from plant physiology to global carbon cycle studies. To gain insight into this puzzle, we excavated whole plant architectures of Nitraria tangutorum Bobrov, a C-3 species that has an exceptional capability of fixing sands and building sand dunes, in two deserts in northwestern China. We systematically and simultaneously measured carbon isotope ratios and nitrogen and phosphorous contents of different parts of the excavated plants. We also determined the seasonal variations in leaf carbon isotope ratios on nearby intact plants of N. tangutorum. We found, for the first time, that higher nitrogen contents in heterotrophic organs were significantly correlated with increased heterotrophic C-13 enrichment compared to leaves. However, phosphorous contents had no effect on the enrichment. In addition, new leaves had carbon isotope ratios similar to roots but were progressively depleted in C-13 as they matured. We concluded that a nitrogen-mediated process, hypothesized to be the refixation of respiratory CO2 by phosphoenolpyruvate (PEP) carboxylase, was responsible for the differences in C-13 enrichment among different heterotrophic organs, while processes such as fractionating foliar metabolism and preferentially loading into phloem of C-13-enriched sugars may contribute to the overall autotrophic-heterotrophic difference in carbon isotope compositions.