“Enzyme latch” and “iron gate” are two essential mechanisms that govern the cycling of soil organic carbon (SOC) in wetlands. However, the specific contributions of these mechanisms to the response of different peatland SOC to water table decline under global warming remain poorly understood. We addressed this knowledge gap by simulating oxygen exposure following water table decline and warming in fen and bog soils and quantifying CO2 emissions. In fen soils, aerobic conditions alone did not significantly increase CO2 emissions in all peat layers, primarily because Fe(II) oxidation inhibited phenol oxidase activity, counterbalancing the stimulating effect of oxygen. Furthermore, Fe-bound OC slowed carbon mineralization. While simultaneous aeration and warming did not affect Fe-bound OC levels, they significantly enhanced phenol oxidase activity throughout the profiles, thereby increasing CO2 emissions. Therefore, both iron protection and enzyme stimulation mediated the changes in CO2 emissions from fen soils under aerobic conditions, with the former dominating without warming and the latter in its presence. In bog soils, aerobic conditions enhanced phenol oxidase activity and CO2 emissions across all layers, regardless of temperature, demonstrating that enzyme activities dominate OC mineralization. In a warming environment, the “enzyme latch” will dominate the fate of peatland soil carbon.