Global climate change experiments have shown changes in productivity, phenology, species composition, and nutrient acquisition and availability; yet, the underlying mechanisms for these responses, especially in multi-factorial experiments, are poorly understood. Altered nutrient availability is a major consequence of global change, directly due to anthropogenic nitrogen (N) deposition, and indirectly due to shifts in temperature and water availability. In the Jasper Ridge Global Change Experiment, microarrays were used to investigate the transcriptional responses of the dominant dicot, Geranium dissectum, to simulated N deposition. The transcript levels for several photosynthetic genes were elevated in plants exposed to elevated N, as has been reported previously, validating the use of microarrays under field conditions. A coordinated response of a suite of genes previously reported to be induced in response to phosphate (Pi) deficiency was observed, including genes for the glycolytic bypass pathway, which reduces ATP and Pi requirements for sugar degradation, suggesting that the plants were phosphorus (P) limited. Confirming this conclusion, foliar P levels in G. dissectum leaves were reduced to levels that are suboptimal for growth in plants grown in elevated N and elevated CO2 plots. Thus, although plants commonly produce more biomass in response to elevated N in native grasslands, this growth response may be suboptimal due to a P limitation. Foliar P levels in plants from elevated CO2 plots were also suboptimal for growth. However, genes indicative of Pi deficiency were not significantly expressed at higher levels. Transcript levels for genes involved in nitrate uptake and assimilation were unchanged by the elevated N deposition treatment, possibly due to the combined impacts of elevated N deposition and P limitation under field conditions. These observations highlight the complexity of the impact of global climate change factors in the field.