Theories of ocean–atmosphere interaction during a Madden–Julian Oscillation (MJO) are generally based on a thermodynamic model with surface fluxes dictating changes in sea surface temperature. Evidence from a two month ocean glider deployment in early 2019 in the southeast Indian Ocean suggests the impact of mesoscale dynamics on upper-ocean stratification likely affects ocean–atmosphere interaction at MJO scales. Until mid-February, local surface fluxes consistent with a convectively suppressed MJO phase drove near-surface ocean evolution. With the advection of a fresh-core eddy to the glider location in late February, ocean dynamics then becomes an additional driver of this evolution by modulating local stratification and generating a barrier layer of ≈12 m thickness for 10 days. One-dimensional modelling experiments based on the ocean and atmospheric conditions experienced during our sampling period show that the ocean subsurface structure within the eddy induce changes in SST of physical significance for ocean-atmosphere interaction. Moreover, results also suggest that the presence of a thick eddy-induced barrier layer during the MJO suppressed phase modulates the magnitude of temperature anomalies forced by surface fluxes during the following enhanced MJO phase. As eddies are abundant in this area, their dynamics must be considered to correctly represent SST variability for MJO modelling.