Over 3000 iron formation caves (IFCs) have formed in erosion-resistant Fe(III)-rich rocks throughout Brazil. Microbial Fe(III) reduction occurs in IFCs, where a microbe-rich, Fe(III)-depleted paste (sub muros) is found behind an Fe(III)-(hydr)oxide crust in the ceiling/walls. Microbial Fe(III) reduction in sub muros appears to be responsible for the transformation of Fe(III) to more soluble Fe(II), which is removed, leading to cave formation. This process of biospeleogenesis is likely controlled by O2 availability, which is linked to seasonal changes. Here, we studied the effects of alternating anoxia/oxia on the microbial community and on Fe solubility in banded iron formation (BIF), a rock type consisting of layered Fe(III)-oxide and silicate. Incubations of synthetic pore water, pulverized BIF, and sub muros were prepared and incubated under anoxia, during which BIF-Fe(III) reduction proceeded. During the Fe(III) reduction period, Firmicutes and/or Alphaproteobacteria were enriched, and genes involved in Fe(III) and sulfate reduction were detected in the metagenomes. Fe(II) oxidation genes, which were detected in the fresh sub muros, were not found. Upon the addition of atmospheric O2, Fe(III) reduction was arrested, and incomplete Fe(II) oxidation occurred. Betaproteobacteria, Gammaproteobacteria, and Chloroflexi increased in relative abundance following aeration, and Fe(III) reduction genes were still identified. Our results demonstrate that the sub muros microbial community retains the ability to reduce Fe(III) and drive speleogenesis despite fluctuations in O2 levels.