Atmosphere‐ocean feedbacks often improve the Madden‐Julian oscillation (MJO) in climate models, but these improvements are balanced by mean state biases that can degrade the MJO through changing the basic state on which the MJO operates. The Super‐Parameterized Community Atmospheric Model (SPCAM3) produces perhaps the best representation of the MJO among contemporary models, which improves further in a coupled configuration (SPCCSM3) despite considerable mean state biases in tropical sea surface temperatures and rainfall. We implement an atmosphere‐ocean‐mixed‐layer configuration of SPCAM3 (SPCAM3‐KPP) and use a flux‐correction technique to isolate the effects of coupling and mean state biases on the MJO. When constrained to the observed ocean mean state, air‐sea coupling does not substantially alter the MJO in SPCAM3, in contrast to previous studies. When constrained to the SPCCSM ocean mean state, SPCAM3‐KPP fails to produce an MJO, in stark contrast to the strong MJO in SPCCSM3. Further KPP simulations demonstrate that the MJO in SPCCSM3 arises from an overly strong sensitivity to El Ni?o–Southern Oscillation events. Our results show that simulated interannual variability and coupled‐model mean state biases affect the perceived response of the MJO to coupling. This is particularly concerning in the context of internal variability in coupled models, as many previous MJO sensitivity studies in coupled models used relatively short (20‐ to 50‐year) simulations that undersample interannual‐decadal variability. Diagnosing the effects of coupling on the MJO requires simulations that carefully control for mean state biases and interannual variability. Plain Language Summary Many studies suggest that feedbacks between the atmosphere and ocean are essential for simulating the Madden‐Julian oscillation, which controls weekly to monthly tropical rainfall. However, model experiments that diagnose the effect of these feedbacks are often not performed in a controlled manner, because introducing atmosphere‐ocean feedbacks changes other aspects of the simulation, including the background climate and phenomena such as the El Ni?o–Southern Oscillation. These changes may affect the Madden‐Julian oscillation as well, separately from direct atmosphere‐ocean feedbacks, but these changes are often erroneously considered part of the sensitivity of the Madden‐Julian oscillation to atmosphere‐ocean feedbacks. We demonstrate that in one model that simulates the Madden‐Julian oscillation well, the Super‐Parameterized Community Atmospheric Model, intraseasonal atmosphere‐ocean feedbacks alone do not substantially alter the Madden‐Julian oscillation. Rather, the previously perceived improvement to the Madden‐Julian oscillation from atmosphere‐ocean feedbacks arises from a too strong response of the Madden‐Julian oscillation to El Ni?o events. Future studies must carefully control for how introducing atmosphere‐ocean feedbacks affects other aspects of the simulation, to better isolate the effect of those feedbacks on the Madden‐Julian oscillation.
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