Records of atmospheric CO₂ and ¹³CO₂ can be used to distinguish terrestrial vs. oceanic exchanges of CO₂ with the atmosphere. However, this approach has proven difficult in the tropics, partly due to extensive land conversion from C₃ to C₄ vegetation. We estimated the effects of such conversion on biosphere-atmosphere ¹³C exchange for 1991–2000, and then explored how this “land-use disequilibrium” altered the partitioning of net atmospheric CO₂ exchanges between ocean and land using NOAA-CMDL data and a 2D, zonally averaged atmospheric transport model. Our results suggest sizable CO₂ uptake in C₃-dominated tropical regions in 8 of the 10 years; 1997 and 1998, which included a strong ENSO event, are near neutral. Since these fluxes include any deforestation source, our findings imply either that such sources are smaller than previously estimated, and/or the existence of a large equatorial terrestrial CO₂ sink.