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Indian Ocean meridional heat transport (MHT_IO) drives climate and ecosystem impacts, through changes to ocean temperature. Improved understanding of natural variability in tropical and subtropical MHT_IO is needed to contextualize observations and future projections. Previous studies suggest that El Niño-Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) can drive variability in MHT_IO. However, it is unclear whether internally generated IOD can drive variability in MHT_IO, or if the apparent relationship between IOD and MHT_IO arises because both are modulated by ENSO. Here, we use a model experiment which dynamically removes ENSO to determine the role of internally forced IOD on MHT_IO. We find that IOD is not linked to anomalies in MHT_IO. Nevertheless, internal atmospheric variability drives significant MHT_IO variability. There is little evidence for decadal or multidecadal variability in MHT_IO, suggesting this may be a region where an anthropogenic trend rises above the level of internal variability sooner.