This paper presents a proposal to use an electrochemical flow-by reactor for hydrogen peroxide electrogeneration using cathodes formed from the incorporation of organic redox catalysts (2-ethylanthraquinone, 2-tert-butylanthraquinone, alizarin, and azobenzene) in the structure of gas diffusion electrodes. These electrodes help circumvent the low solubility of oxygen in aqueous solutions. Organic redox catalysts, which typically contain quinone or azo groups in their structure, were added to the electrode mass in a 10% proportion. The electrodes were used to study the electrogeneration of hydrogen peroxide in situ, in an acid medium (0.1 mol L-1 H2SO4 and 0.1 mol L-1 K2SO4, pH 1), inside an electrochemical flow-by reactor. Comparative analysis among the different catalysts indicated that the best electrode for hydrogen peroxide electrogeneration was the gas diffusion electrode modified with 10% of 2-ethylanthraquinone. With an underflow rate of 200 L h-1, hydrogen peroxide was formed with a maximum yield of 998.12 mg L-1 after 2 h at -2.0 V vs Pt//Ag/AgCl, for which the energy consumption was 11.21 kWh kg-1. The use of the electrochemical flow-by reactor was much more efficient, in that it yielded higher concentrations of hydrogen peroxide with extremely low energy consumption, compared to that obtained when using an electrochemical cell. In addition, for ensuring appropriate usage of the electrodes, optimizing their potential for the maximum generation of hydrogen peroxide, and obtaining the highest efficiency for the reduction of oxygen, a fuzzy algorithm was developed to help support the user’s decision.