Next generation renewable biofuels that are compatible with current infrastructure and support the heavy transportation sector, where ethanol is non-viable, are strategically important targets for biofuel research. One route to highly reduced fuel molecules is by microbial conversion of hydrolyzed cellulosic sugars to free fatty acids, which are a useful precursor for downstream catalytic or enzymatic conversions to alkanes, olefins, fatty alcohols, or fatty acid esters. In particular, expression of an acyl-acyl carrier protein thioesterase in E. coli results in increased flux through fatty acid biosynthesis and the accumulation of moderate titers of free fatty acids. However a next-generation strain has not yet been engineered that can achieve greater than 30% of the maximum theoretical yield on any carbon source. It was found that endogenous fatty acid production specifically results in large reductions in cell viability, compromised inner membrane integrity, and changes in cell morphology. To determine a functional basis for these observations, a differential transcriptomic, proteomic, and lipidomic analysis was undertaken comparing a fatty acid overproducing strain to a non-overproducing strain, with the goal of determining potential stress responses and metabolic perturbations. Some key findings were induction of the genes encoding phage shock proteins, which are induced under conditions that cause dissipation of the proton motive force; induction of the MarA/Rob/SoxS regulons, which are induced by small toxic molecules or oxidative stress; and a greatly increased degree of unsaturation in long chain fatty acids accompanied by down-regulation of genes involved in unsaturated fatty acid biosynthesis. These findings and successive iterations of strain engineering based on these results will be discussed.