Cellular hosts are widely used for the production of chemical compounds including pharmaceutics, fuels, and specialty chemicals. Strain engineering focuses on manipulating and improving these hosts for new and enhanced functionalities including increased titers and better bioreactor performance. These tasks have traditionally been accomplished using a combination of random mutation, screening and selection, and metabolic engineering. However, common metabolic engineering techniques are limited in their capacity to elicit multigenic, complex phenotypes. These phenotypes can also include nonpathway-based traits such as tolerance and productivity. Global transcription machinery engineering (gTME) is a generic methodology for engineering strains with these complex cellular phenotypes. In gTME, dominant mutant alleles of a transcription-related protein are screened for their ability to reprogram cellular metabolism and regulation, resulting in a unique and desired phenotype. gTME has been successfully applied to both prokaryotic and eukaryotic systems, resulting in improved environmental tolerances, metabolite production, and substrate utilization. The underlying principle involves creating mutant libraries of transcription factors, screening for a desired phenotype, and iterating the process in a directed evolution fashion. The successes of this approach and details for its implementation and application are described here.