The direct conversion of low concentrations of CO2 is an essential approach, considering the expensive gas conditioning process for pure CO2, but has not yet been intensely studied in a membrane electrode assembly (MEA) electrolyzer. Herein, we explored the CO2 reduction with various CO2 concentrations in a zero-gap MEA electrolyzer and found that suppressing the hydrogen evolution reaction (HER) became more critical at low concentrations of CO2. We demonstrate that a Ni single-atom (Ni-N/C) catalyst exhibits a high tolerance toward low CO2 partial pressure (PCO2) because of the intrinsically large activation energy of the HER. Ni-N/C outperformed the CO productivity of Ag nanoparticles, especially at low concentrations of CO2 in the zero-gap MEA. When the PCO2 was lowered from 1.0 to 0.1 atm, Ni-N/C maintained >93% of CO Faradaic efficiency (FECO), but Ag nanoparticles showed a decrease in FECO from 94% to 40%. Furthermore, on the basis of a computational fluid dynamics simulation, we developed extrinsic operating conditions controlling the water transfer from the anolyte to the catalyst layer and improved CO selectivity at low CO2 concentrations in the MEA electrolyzer.