Carbon isotope fractionation in metabolic processes following carboxylation of ribulose-1,5-bisphosphate (RuBP) is not as well described as the discrimination during photosynthetic CO2 fixation. However, post-carboxylation fractionation can influence the diel variation of δ13C of leaf-exported organic matter and can cause inter-organ differences in δ13C. To obtain a more mechanistic understanding of post-carboxylation modification of the isotopic signal as governed by physiological and environmental controls, we combined the modelling approach of Tcherkez et al., which describes the isotopic fractionation in primary metabolism with the experimental determination of δ13C in leaf and phloem sap and root carbon pools during a full diel course. There was a strong diel variation of leaf water-soluble organic matter and phloem sap sugars with relatively 13C depleted carbon produced and exported during the day and enriched carbon during the night. The isotopic modelling approach reproduces the experimentally determined day–night differences in δ13C of leaf-exported carbon in Ricinus communis. These findings support the idea that patterns of transitory starch accumulation and remobilization govern the diel rhythm of δ13C in organic matter exported by leaves. Integrated over the whole 24 h day, leaf-exported carbon was enriched in 13C as compared with the primary assimilates. This may contribute to the well-known – yet poorly explained – relative 13C depletion of autotrophic organs compared with other plant parts. We thus emphasize the need to consider post-carboxylation fractionations for studies that use δ13C for assessing environmental effects like water availability on ratio of mole fractions of CO2 inside and outside the leaf (e.g. tree ring studies), or for partitioning of CO2 fluxes at the ecosystem level.