We investigated the molecular basis of the long-term adaptation to nitrogen (N) limitation of wheat plants grown in a simulated crop canopy, with a focus on the stage when carbon (C) reserves are accumulated in stems for later remobilization to grain. A cDNA microarray representing approximately 36,000 unique sequences was used to compare gene expression in a number of above-ground organs at anthesis. Fructan accumulation in stems was accompanied by elevated transcripts for a suite of fructosyltransferases (FTs) and for a fructan 6-exohydrolase (6-FEH) in the low N compared to high N stems. Clustering analysis identified a grouping that included several FTs and a number of genes thought to be involved in regulation of storage C metabolism or senescence in other systems. Transcripts for three FTs and for 6-FEH increased, while transcripts for 1-FEH decreased, in sucrose-fed wheat stems compared to controls. The opposite trends were seen for these transcripts in wheat stems fed ABA. Of the putative regulators, only transcripts for the WPK4 kinase increased in response to sucrose, suggesting a role for this kinase in C storage metabolism in the reproductive wheat stems grown in low N. This work represents the first large-scale transcriptome study of responses to the most common nutrient limitation in one of the world's most economically important crops.