The effect of high temperature (HT) stress on nicotine biosynthesis in Nicotiana attenuata was examined. Nicotine content was measured in mature leaves, young sink leaves and in roots from well-watered plants grown at 25 °C as controls and from plants exposed to 38 °C and 43 °C temperatures applied for 24, 48, 72 and 96-hr duration. At 38 °C, all leaf nicotine levels were significantly less than control plants for up to 72-hr exposure but rose sharply thereafter to levels significantly greater than controls with 96-hr exposure. In contrast, plants exposed to 43 °C never exhibited a reduction in leaf nicotine content and showed a significant increase in content with just 48-hr exposure. When radioactive 11CO2 was administered to plants, HT stress significantly reduced fixation. Furthermore, radiocarbon flux analysis revealed that ‘new’ C partitioning (as 11C) into the [11C]-amino acid pool was significantly reduced with HT stress as were yields of [11C]-aspartic acid, an important amino acid in nicotine biosynthesis, and its beta-amido counterpart [11C]-asparagine significantly reduced. In contrast, [12C]-aspartic acid levels appeared unaffected at 38 °C but were significantly elevated at 43 °C relative to controls. Additionally, [12C]-asparagine levels were significantly elevated at both stress temperatures. Finally, leaf total soluble protein (TSP) was reduced 39% with long exposures to both stress temperatures. However, Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which was 41% TSP appeared unaffected by HT stress. Altogether, these results support the theory that plant proteins other than Rubisco degrade at elevated temperatures freeing up essential amino acids supporting the nicotine biosynthetic machinery, and while feedback might downregulate de novo amino acid synthesis from ‘new’ C resources, more than likely plant C/N rebalancing caused by HT reductions in C input restricted N uptake, which in turn, limited this process.