Increasing evidence has shown that the reaction of zero-valent iron [Fe(0)] by oxygen can produce strong oxidants and rapidly oxidize the tractable contaminants. However, Fe(0) is vulnerable to passivation in the presence of oxygen, which significantly decreases its surface reactivity towards the removal of refractory contaminants. Microorganisms capable of reducing ferric iron in the presence of oxygen are expected to overcome the limitation of Fe(0) passivation. However, no studies to date have shown that microorganisms are able to depassivate Fe(0) for the removal of recalcitrant compounds in the presence of oxygen. In this study, we demonstrated that the carotenoid-producing Sphingobium hydrophobicum C1 was able to significantly enhance the removal of deca-brominated diphenyl ether by depassivating Fe(0) and subsequently removing the newly formed metabolites under semi-aerobic conditions (> 4 mg/L oxygen). S. hydrophobicum C1 effectively depassivated Fe(0) and regenerated its reactivity by reducing ferric iron under semi-aerobic conditions. Some unique characteristics of S. hydrophobicum C1, including the presence of membrane-integrated carotenoids and certain cell proteins, were essential for the ferric iron reduction of S. hydrophobicum C1 in the presence of oxygen. Our results may provide new insights into the bioremediation of persistent pollutants and will contribute to future studies to enhance our understanding of microbial iron reduction.