Systems metabolic engineering has made the renewable production of industrial chemicals a feasible alternative to modern operations. One major example of a renewable process is the production of carboxylic acids, such as octanoic acid (C8), from Escherichia coli, engineered to express thioesterase enzymes. C8, however, is toxic to E. coli above a certain concentration, which limits the final titer. C-13 metabolic flux analysis of E. coli was performed for both C8 stress and control conditions using NMR2Flux with isotopomer balancing. A mixture of labeled and unlabeled glucose was used as the sole carbon source for bacterial growth for C-13 flux analysis. By comparing the metabolic flux maps of the control condition and C8 stress condition, pathways that were altered under the stress condition were identified. C8 stress was found to reduce carbon flux in several pathways: the tricarboxylic acid (TCA) cycle, the CO2 production, and the pyruvate dehydrogenase pathway. Meanwhile, a few pathways became more active: the pyruvate oxidative pathway, and the extracellular acetate production. These results were statistically significant for three biological replicates between the control condition and C8 stress. As a working hypothesis, the following causes are proposed to be the main causes for growth inhibition and flux alteration for a cell under stress: membrane disruption, low activity of electron transport chain, and the activation of the pyruvate dehydrogenase regulator (PdhR).