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. Heat stored in the upper ocean can have important implications for the interaction between the ocean and the atmosphere. The tropical Indian Ocean is unique in that it is where one of the strongest sources of large-scale atmospheric convection known as the Madden-Julian Oscillation (MJO) typically originates on timescales ranging from 1 to 3 months. The MJO moves eastward exerting stresses on the ocean surface that generates planetary-scale waves. The waves generated on these timescales largely propagate eastward along the equator and westward slightly off the equator. In this study, we investigate the MJO's impact on the upper Ocean Heat Content (OHC) and the different mechanisms causing it to vary. In the upper 200 m of the ocean, ocean currents and temperature contrasts in the east-west direction are important in driving changes of OHC along the equator while slightly off the equator, ocean currents and temperature contrasts in the north-south direction become more important. Ocean temperature anomalies are also found to be produced by the MJO forced waves. The ocean heat content anomalies move eastward along the equator and westward slightly off the equator and have the strongest signal at depths of between 50-150 m. A dynamically and kinematically consistent ocean state estimate is used to investigate subseasonal Ocean Heat Content (OHC) variability Horizontal advection is the main driver of upper OHC variability throughout most of the Indian Ocean The Madden-Julian Oscillation drives equatorial OHC by means of oceanic Kelvin waves and Rossby waves