In the equatorial Indian Ocean, the largest subseasonal temperature variations in the upper ocean are observed below the mixed layer. Subsurface processes can influence mixed layer temperature and consequently air‐sea coupling. However, the physical processes driving temperature variability at these depths are not well quantified. During the boreal winter, the Madden–Julian Oscillation (MJO) partly drives upper ocean heat content (OHC) variations. Therefore, to understand processes driving subseasonal OHC variability in the equatorial Indian Ocean, we use an observationally constrained, physically consistent ocean state estimate from the Estimating the Circulation and Climate of the Ocean (ECCO) Consortium. Using a heat budget analysis, we show that the main driver of subseasonal OHC variability in the ECCO ocean state estimate is horizontal advection. Along the equator, OHC variations are driven by zonal advection while the role of meridional advection becomes more important away from the equator. During the active phase of the MJO, net air‐sea heat fluxes damp OHC variability along the equator, while away from the equator net air‐sea heat fluxes partly drive OHC variability. Equatorial OHC variations are found to be associated with processes driven by Kelvin and Rossby waves consistent with previous studies. By quantifying the physical processes, we highlight the important role of ocean dynamics in contributing to the observed variations of subseasonal OHC in the equatorial Indian Ocean.