Yeast recycling, which is a common practice in sugarcane ethanol plants, could be expanded if it could be successfully implemented in corn-based ethanol production. However, the process of recycling the yeast remaining after fermentation is hampered by contaminating microorganisms that reduce the fermentation efficiency and compete with the yeast for the fermentable sugars. Currently, antibiotics are used to control microbial contamination. This study proposes chlorine dioxide and electron beam irradiation as alternative control methods for completely inactivating contaminants and minimizing their effect on recycled yeast. For that, wort sterilization using electron radiation (20 kGy) and treatment with a chemical biocide, namely chlorine dioxide (125 mg kg−1), were compared with non-treated wort. Five fermentation cycles were performed using fed-batch systems with 300 g L−1 of fermentable sugars. The results obtained in this study showed the inactivation of contaminants under the effect of electron beam irradiation, which led to an increase in the productivity, yield, and efficiency of fermentation by 0.21 g L−1h−1, 2.6%, and 4.7%, respectively. However, ClO2 did not show promising results in reducing contamination or improving fermentative parameters. Thus, electron beam irradiation of contaminated wort may be a suitable alternative to chemical biocides and would allow the use of recycled yeast in corn-based ethanol plants.