Cotton is a perennial plant grown as an annual row crop in much of the world. Cotton stems and roots store starch prior to reproduction that is subsequently available to support reproduction. Aspects of nitrogen metabolism in cotton stems and roots were investigated to determine whether these tissues also provided nitrogen to support reproduction. Measurements of total nitrogen, soluble proteins, and individual amino acids indicated that nitrogen metabolism was altered after flowering began. Analysis of gene expression from previous microarray experiments also showed patterns consistent with a role of altered nitrogen metabolism during seed set. Changes in transcript levels of genes associated with amino acid biosynthesis, biosynthesis of nitrogenous compounds, and protein turnover also indicated that nitrogen metabolism changed in roots during seed set. We confirm that stem and roots provide nitrogen to support reproduction, and propose that the transport of nitrogenous compounds from these tissues to reproductive tissue could affect seed set by communicating the nitrogen status of the plant.