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Abstract The TEX₈₆proxy, based on the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) from planktonic Thaumarchaeota, is widely used to reconstruct sea surface temperature (SST). Recent observations of species‐specific and regionally dependent TEX₈₆‐SST relationships in cultures and the modern ocean raise the question of whether nonthermal factors may have impacted TEX₈₆paleorecords. Here we evaluate the effects of ecological changes on TEX₈₆using one Pliocene and two Pleistocene sapropels from the Mediterranean Sea. We find that TEX₈₆‐derived SSTs deviate from‐derived SSTs before, during, and after each sapropel event.‐derived SSTs vary by less than 6 °C, while TEX₈₆‐derived SSTs vary by up to 15 °C within a single record. Compound‐specific carbon isotope compositions indicate minimal confounding influence on TEX₈₆from exogenous sources. Some of the variation can be accounted for by changes in nitrogen cycling intensity affecting thaumarchaeal iGDGT biosynthesis, as demonstrated by an inverse relationship between TEX₈₆and δ¹⁵N_TN. TEX₈₆‐derived SSTs also consistently show warm anomalies in the Pleistocene, while the Pliocene samples exhibit both warmer and cooler relative offsets. These anomalies result from systematic differences between Plio‐Pleistocene iGDGT distributions and both modern Mediterranean and modern, globally distributed core top samples. Through characteristic GDGT distributions, we suggest the existence of three distinct endemic populations of Thaumarchaeota in the Pliocene, Pleistocene, and modern Mediterranean Sea, respectively. Importantly, these communities prevailed during both sapropel and oligotrophic conditions. Our results demonstrate that ecological and community‐specific effects must be considered when applying the TEX₈₆proxy to paleorecords.