We examined the timeline by which methyl jasmonate (MeJA) reprograms new carbon partitioning into key metabolite pools. The radioactive isotope ¹¹C (t(¹/₂) 20.4 min), administered to intact leaves of Nicotiana tabacum L. (cv Samsun) as ¹¹CO(2) gas enabled us to measure changes in new carbon partitioning into soluble sugar and amino acid pools of [¹¹C]photosynthate. A 500 μM MeJA treatment resulted in a decrease in the [¹¹C]soluble sugar pool and an increase in the [¹¹C]amino acid pool after 4 h. This pattern was more pronounced 15 h after treatment. We also examined the timeline for ¹¹C-partitioning into aromatic amino acid metabolites of the shikimate pathway. [¹¹C]Tyrosine, [C¹¹C]phenylalanine and [¹¹C]tryptophan were elevated 1.5-fold, 12-fold and 12-fold, respectively, relative to controls, 4 h after MeJA treatment, while endogeneous pools were unchanged. This suggests that only new carbon is utilized during early stages of defense induction. By 15 h, [C¹¹C]tyrosine and [¹¹C]phenylalanine returned to baseline while [¹¹C]tryptophan was elevated 30-fold, suggesting that MeJA exerts selective control over the shikimate pathway. Finally, we measured trans-cinnamic acid levels as a gauge of downstream phenolic metabolism. Levels were unchanged 4 h after MeJA treatment relative to controls, but were increased 2-fold by 15 h, indicating a lag in response of secondary metabolism.