Acetate is a toxic by-product of glucose metabolism in Escherichia coli. In the present work, endogenous metabolic networks of E. coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA. In conjunction with the elevation of acetyl-CoA carboxylase level, the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids. Together with overexpression of acetyl-CoA carboxylase (ACC) subunits from Photorhabdus luminescens (PlACC), amplification of the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) resulted in high level production of three flavonoids tested. Overall, the metabolic engineering of central metabolic pathways described in the present work increased the production of naringenin, eriodictyol, and pinocembrin up to 183%, 373%, and 1379% respectively over control strains in 40 h, which corresponded to 119 mg/L, 52 mg/L, and 429 mg/L. The elevation of the low affinity acetate pathway comprising of phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid production. It is evident that metabolic engineering methods to recycle waste products can be used to improve the production of high-value heterologous metabolites.