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Abstract Key features of late Neogene climate remain uncertain due to conflicting records derived from different sea surface temperature (SST) proxies. To understand scenarios in which proxy‐derived temperature estimates can be used interchangeably or are instead measuring different aspects of the same system, it is necessary to explore both the consistencies and differences between specific paleothermometers. Here, we report orbital‐scale climate records from ODP Site 846 in the eastern equatorial Pacific (EEP) for the interval from ~5–6 Ma using alkenone and archaeal lipid paleothermometers. Results from both proxies are similar in their secular trends and magnitude of long‐term temperature change, and spectral analysis demonstrates that the records are coherent and in‐phase in both the obliquity and precession bands. However, we find that the temperatures reconstructed by TEX₈₆are consistently offset toward colder values by ~2 °C relative to U^k′₃₇‐derived temperatures in global calibrations, or by ~0.8 °C in Bayesian‐based calibrations. All combinations of calibrations also yield approximately twice the amplitude of orbital‐scale variation in TEX₈₆relative to U^k′₃₇‐derived temperature fluctuations. Both temperature proxies are negatively correlated with sedimentary alkenone concentrations, which we use as an indicator of increased export productivity. Removing this productivity contribution from TEX₈₆results in an adjusted TEX₈₆record with temperature sensitivity identical to U^k′₃₇. In future applications, this signal may be decoupled using additional sedimentary indicators of paleoproductivity, which likely will be most important for upwelling zone environments. There remain other nonexplained factors that contribute to differences between TEX₈₆and U^k′₃₇that warrant additional investigation.