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The Indonesian Throughflow (ITF) is a critical conduit for the inflow of Pacific waters into the Indian Ocean. It has long been considered a potential switch in controlling global climate events. Previous work has primarily focused on Pleistocene glacial-interglacial variability, and there have been few records of ITF variability from the highly dynamic Late Miocene period. In this study, we present two new high-resolution sea surface temperature (SST) records from Site U1482 spanning the Late Miocene Cooling (LMC) to investigate the changing dynamics in the ITF between 8-4 Ma. The two records we have used are based on Mg/Ca analysis of Trilobatus sacculifer and on TEX86. One limitation of many studies is that Mg/Ca analysis has been performed at much higher resolution than TEX86. However, here, owing to the high preservation of glycerol dialkyl glycerol tetraethers (GDGTs), we were able to reconstruct TEX86-derived temperatures at about 21 ka resolution high enough to match cycles in Mg/Ca-derived SST. Before the LMC, there is a strong connection between the two records. Both records show the major cooling event around 6.5 Ma associated with the LMC as well as prominent transient cooling events between 6.5-5.5 Ma. However, in the early Pliocene at 5.2 Ma, the two records diverge markedly, with the Mg/Ca-based record recording several cooling episodes that are not reflected in the TEX86 data. Based on previous work, the TEX86H proxy, which employs a nonlinear fit to better reflect SSTs above those of the modern era, matches Austral Summer SSTs in this region. Interestingly, the TEX86H data at this point aligns more closely with temperature trends in the West Pacific Warm Pool (WPWP) than local Mg/Ca. Given that the TEX86H data have been interpreted as Austral summer SSTs, this suggests that in the Early Pliocene, there was a shift in the ITF, allowing seasonal throughflow directly from the WPWP. Given that the WPWP currently exerts little influence, this shift has critical implications for ocean circulation and for the impact of the end of the LMC and the onset of the very warm Early Pliocene. This may help explain the rapid warming at the end of the LMC. It also demonstrates the importance of multi-proxy analysis being done at a similar resolution.