Methods for controlling the growth of bacteria in ethanol fermentation systems with antibiotic alternatives, which can be nonoxidizing biocides, stabilized oxidizers, or any combinations thereof, are described. As an option, a process or composition of the present invention can include one or more polycyclic antibacterial peptides. The methods can provide improvements, such as increased ethanol yields with minimal carryover of biocide into co-products of the processes.