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A controversial aspect of Pliocene (5.3–2.6 Ma) climate is whether El Niño‐like (El Padre) conditions, characterized by a reduced trans‐equatorial sea‐surface temperature (SST) gradient, prevailed across the Pacific. Evidence for El Padre is chiefly based on reconstructions of sea‐surface conditions derived from the oxygen isotope (δ¹⁸O) and Mg/Ca compositions of shells belonging to the planktic foraminiferTrilobatus sacculifer. However, fossil shells of this species are a mixture of multiple carbonate phases—pre‐gametogenic, gametogenic (reproductive), and diagenetic calcites—that formed under different physiological and/or environmental conditions and are averaged in conventional whole‐shell analyses. Through in situ measurements of micrometer‐scale domains within Pliocene‐aged shells ofT. sacculiferfrom Ocean Drilling Program Site 806 in the western equatorial Pacific, we show that the δ¹⁸O of gametogenic calcite is 0.6–0.8‰ higher than pre‐gametogenic calcite, while the Mg/Ca ratios of these two phases are the same. Both the whole‐shell and pre‐gametogenic Mg/Ca records indicate that average early Pliocene SSTs were ~1°C warmer than modern, with present‐day SSTs being established during the latest Pliocene and early Pleistocene (~3.0–2.0 Ma). The measurement of multiple calcite phases by whole‐shell δ¹⁸O analyses masks a late Pliocene to earliest Pleistocene (3.6–2.2 Ma) decrease in seawater δ¹⁸O (δ¹⁸O_sw) values reconstructed from in situ pre‐gametogenic δ¹⁸O and Mg/Ca measurements. Our novel δ¹⁸O_swrecord indicates that sea‐surface salinities in the west Pacific warm pool were higher than modern prior to ~3.5 Ma, which is consistent with more arid conditions under an El Padre state.