The generation of ozone microbubbles (O3MB) is an effective means of sterilizing plant culture media against bacteria and pathogens; however, the use of O3MB can induce precipitation of metal ions from the medium, such as iron (Fe) and manganese (Mn), that are important to plant growth. Here, we evaluated whether addition of a chelator, either ethylenediaminetetraacetic acid (EDTA) or diethylenetriaminepentaacetic acid (DTPA), could prevent this side effect of O3MB sterilization. We compared nutrient composition, medium sterility, and plant growth after various treatments (0, 0.1, 0.01, 0.001, or 0.0001% (w/v) of EDTA and DTPA addition after O3MB generation). Metal chelators (EDTA and DTPA) are widely used in algal and plant growth solutions to maintain iron (Fe) solubility in hydroponic solutions, EDTA is used in agriculture to remove heavy metals from heavily contaminated soils and also as a plant fertilizer, and DTPA has a wide range of applications including removal of heavy metals from agricultural soils. Thus, the available evidence indicates that addition of a chelator after O3MB generation may prevent precipitation of oxidized Fe or Mn in a culture medium. The addition of a chelator resulted in a concentration-dependent reduction in precipitates and the maintenance of Fe and Mn concentrations in the medium. Although O3MB sterilization did not affect plant growth, the addition of a chelator at concentrations of 0.1, 0.01, or 0.001% (w/v) had a significant deleterious effect. However, at a concentration of 0.0001%, the chelator had no significant effect on plant growth but did result in the maintenance of a higher Fe and Mn concentration compared to the O3MB treated control. The addition of a chelator did not alter the sterilizing effects of O3MB. These results indicate that the addition of a chelator at a concentration of 0.0001% to an O3MB-sterilized culture medium enabled the retention of dissolved Fe and Mn without affecting plant growth. The use of O3MB, plus a chelator, is an effective disinfection method in hydroponic culture.