Abstract The influence of carbon dioxide (CO 2 ) and soil fertility on the physiological performance of plants has been extensively studied, but their combined effect is notoriously difficult to predict. Using Coffea arabica as a model tree species, we observed an additive effect on growth, by which aboveground productivity was highest under elevated CO 2 and ammonium fertilization, while nitrate fertilization favored greater belowground biomass allocation regardless of CO 2 concentration. A pulse of labelled gases ( 13 CO 2 and 15 NH 3 ) was administered to these trees as a means to determine the legacy effect of CO 2 level and soil nitrogen form on foliar gas uptake and translocation. Surprisingly, trees with the largest aboveground biomass assimilated significantly less NH 3 than the smaller trees. This was partly explained by declines in stomatal conductance in plants grown under elevated CO 2 . However, unlike the 13 CO 2 pulse, assimilation and transport of the 15 NH 3 pulse to shoots and roots varied as a function of interactions between stomatal conductance and direct plant response to the form of soil nitrogen, observed as differences in tissue nitrogen content and biomass allocation. Nitrogen form is therefore an intrinsic component of physiological responses to atmospheric change, including assimilation of gaseous nitrogen as influenced by plant growth history.