A single-column model approach conducted in the context of the Madden–Julian Oscillation through the CINDY2011/Dynamics of the Madden–Julian Oscillation field campaign is used to disentangle the respective role of the parameterizations of surface turbulent fluxes and of model atmospheric physics in controlling the surface latent heat flux. The major differences between the models used in this study occur during the suppressed phases of deep convection. They are attributed to differences in model atmospheric physics which is shown to control the near-surface relative humidity and thereby the surface latent heat flux. In contrast, during active phases of deep convection, turbulent air-sea flux parameterizations impact the latent heat flux through the drag coefficient and can represent two thirds of the divergence caused by the different atmospheric physics. The combined effects need to be accounted for to improve both the representation of latent heat flux and the atmospheric variables used to compute it. ©2019. American Geophysical Union. All Rights Reserved.