Temporal redox fluctuations alter the pools of reducible FeIII and greenhouse gas emissions in humid upland soils. However, it is less clear how the characteristics of these fluctuations (length, frequency, amplitude) impact biogeochemical rates. We hypothesized that anaerobic rates of FeIII reduction and CH4 emissions are sensitive to the length of soil oxygen deprivation. To test this hypothesis, we exposed a surface soil from the Luquillo Experimental Forest to three lengths of O2 perturbation during repeated redox oscillations: an anoxic interval of 6 d with oxic intervals of 8, 24, or 72 h. We found that shorter oxic intervals resulted in more anaerobic FeIII reduction, while longer oxic intervals stimulated higher anaerobic CH4 emissions (CO2 fluxes did not change). We propose that short O2 pulses stimulate Fe reduction by resupplying the FeIII electron acceptor, but do not last long enough to inhibit microbial Fe reducers; conversely long O2 pulses suppress microbial iron reducers to a greater extent than methanogens leading to enhanced CH4 emissions. Thus, the length of periodic oxidant exposure selectively enhances less thermodynamically favorable anaerobic processes by modulating the competitiveness of dominate anaerobic bacteria, which is important for regulating greenhouse gas emissions in redox dynamic soils.