Acetogen strain Clostridium sp. MT1121 produced 300 mM acetate (p < 0.005) and 321 mM ethanol (p < 0.005) from synthesis gas (syngas) blend 60 % CO and 40 % H-2. Clostridium sp. MT1121 was metabolically engineered to eliminate production of either acetate or acetaldehyde during syngas fermentation. We used Cre-lox66/lox71-based gene removal system to eliminate either phosphotransacetylase (pta), or acetaldehyde dehydrogenase (aldh). The resulted biocatalyst with eliminated pta increased ethanol yield to 610 mM (p < 0.005). Inactivation of pta rendered only 502 mM of ethanol (p < 0.005). The acetogen biocatalyst with eliminated aldh produced 450 mM acetate (p < 0.005). The role of cell energy pool preservation for re-directed carbon flux is discussed. This is the first report on time- and cost-efficient gene elimination in acetogens using lox66/lox71 gene elimination system.