Human endeavours into deep space exploration and the prospects of establishing colonies on nearby planets would invariably involve components of bioregenerative life support for food production, cabin atmosphere renewal, and waste recycling. Growing plants and their microbiomes in porous media under different gravitational fields may present new challenges due to effects of liquid distribution on gaseous exchange with roots and microorganisms. We provide the first direct evidence that capillary driven liquid reconfiguration in porous media under reduced gravity conditions reduces oxygen diffusion pathways and enhances anoxic conditions within bacterial hotspots. Parabolic flight experiments using model porous media inoculated with aerobic and facultative anaerobic bacteria reveal the systematic enhancement of anoxic conditions during the reduced gravity periods in the presence but not in the absence of bacterial activity. The promotion of anoxic conditions under reduced gravity may lead to higher nitrous oxide and methane emissions relative to Earth conditions, on the other hand, anoxic conditions could be beneficial for perchlorate bioremediation of Martian soil. The results highlight changes in soil bacterial microhabitats under reduced gravity and the challenges of managing bioregenerative life support systems in space.