Here we present benthic foraminiferal counts, Mg/Ca-based bottom water temperature (BWT) estimates, and benthic stable oxygen and carbon (δ18O and δ13C) isotope records for the early-middle Miocene interval of sites located in the equatorial Pacific Ocean. Benthic foraminiferal counts and accumulation rates are reported for Integrated Ocean Drilling Program (IODP) Sites U1337 and U1338; total assemblages counts were performed in the >150 µm grain size sediment fractions and Epistominella exigua counts were carried out in the >63 µm grain size sediment fractions. Mg/Ca ratios were measured on Oridorsalis umbonatus and used to estimated BWTs at Sites U1337 and U1338, and at Ocean Drilling Project (ODP) Site 1146. For intervals where Mg/Ca ratios could have been affected by carbonate dissolution, we did not estimate BWTs and reported only the Mg/Ca ratios. Benthic stable oxygen and carbon isotope records were measured on Cibicidoides mundulus/C. wuellerstorfi at Site U1338. Our datasets allow to reconstruct BWT changes and reorganizations among benthic foraminiferal assemblages during the Miocene Climatic Optimum and middle Miocene climatic transition in the eastern and western Equatorial Pacific Ocean.