Though chlorine dioxide is generally used to control bacterial contamination, a method was developed which allows the use of stabilized chlorine dioxide (SCD) for controlling contamination during fermentation that uses the bacteria Zymomonas as the biocatalyst, even though Zymomonas is sensitive to chlorine dioxide. Parameters were identified for inoculating a composition for fermentation with Zymomonas cells after a time period has elapsed following SCD addition.