Soil redox conditions exert substantial influence on biogeochemical processes in terrestrial ecosystems. Humid tropical forest soils are often characterized by fluctuating redox, yet how these dynamics affect patterns of organic matter decomposition and associated CO2 fluxes remains poorly understood. We used a 13C-label incubation experiment in a humid tropical forest soil to follow the decomposition of plant litter and soil organic matter (SOM) in response to four redox regimes—static oxic or anoxic, and two oscillating treatments. We used high-resolution mass spectrometry to characterize the relative composition of organic compound classes in the water extractable OM. CO2 production from litter and SOM showed different responses to redox treatments. While cumulative production of SOM-derived CO2 was positively correlated with the length of oxic exposure (r = 0.89, n = 20), cumulative 13C-litter-derived CO2 production was not linked to oxygen availability. Litter-derived CO2 production was highest under static anoxic conditions in the first half of the experiment, and later dropped to the lowest rate amongst the treatments. In anoxic soils, we observed depletion of more oxidized water-extractable OM (especially amino sugar-, carbohydrate-, and protein-like compounds) over the second half of the experiment, which likely served as substrates for anaerobic CO2 production. Results from two-pool kinetic modeling showed that more frequent anoxic exposure limited decomposition of a slow-cycling C pool, but not a fast-cycling pool. These results suggest that aerobic and anaerobic heterotrophs were equally effective at degrading labile substrates released from fresh plant litter in this humid tropical forest soil, while aerobic decomposers were more effective in breaking down the potentially refractory compounds found in SOM.