Anaerobic fermentation of organic compounds is used in many biotechnological processes and has been the subject of much research. A variety of process conditions and different growth media can be used to obtain microbial metabolites. The media must be free from contamination before fermentation. Sterilization is most often achieved by applying heat or other treatments, such as ozonation. Sterilization of liquid media using ozone can be very beneficial, but this method introduces high concentrations of residual oxygen, which inhibit anaerobic processes. Deoxidation is therefore necessary to remove the oxygen from ozonated broths. This study evaluates the effectiveness of three deoxidation agents for two kinds of fermentation media based on malt or molasses: ultrasound, iron(II) sulfate, and Metschnikowia sp. yeast. The time needed for deoxidation varied, depending on the kind of broth and the deoxidation agent. In general, the dynamics of oxygen removal were faster in malt broth. A comparative analysis showed that yeast biomass was the most effective agent, achieving deoxidation in the shortest time. Moreover, the fully deoxidated broth was supplemented with yeast biomass, which is rich in biogenic substrates, expressed as a protein content of 0.13–0.73 g/L. Application of Metschnikowia sp. may therefore be considered as an effective strategy for simultaneous deoxidation and nutrient supplementation of broths used in anaerobic biotechnological processes.