Corn and sugarcane are the primary feedstocks for ethanol production, but microbial contamination hinders yeast fermentation efficiency. Current control methods include antibiotics and sulfuric acid, but they have limitations, resulting in dependence on external inputs and the risk of antibiotic-resistant bacteria. This review examines electron beam technology as an industrial-scale disinfection solution for both corn- and sugarcane-based ethanol production, highlighting its advantages, limitations and opportunities for adoption in Brazil. A critical evaluation highlights the importance of optimal operating conditions for scalability, cost effectiveness and sustainable implementation. Through a practical example, we demonstrate the effectiveness of electron beam treatment in improving fermentation efficiency and reducing contamination-related losses. Notably, the ionizing radiation from this process does not affect wort sugar content or generate radioactive residues. While acknowledging the potentially high energy input requirements, cogeneration in sugarcane mills can address this, making it a viable option; however, further technical and economic evaluation should be made. In addition, electron beam technology is a promising approach for the production of high-value products such as neutral alcohol, amino acids, animal feed and pharmaceuticals. Therefore, this comprehensive review provides valuable insights for researchers, industry stakeholders and policymakers to promote sustainable and efficient ethanol production practices.