Sediment cores from the volcanic Emperor Seamount Chain obtained during RV SONNE cruise SO264 (SONNE-EMPEROR) in August 2018 allow us to reconstruct lateral changes in the subarctic and subtropical gyres in the pelagic North Pacific over the last ~3.4 million years. This dataset comprises benthic stable carbon (δ13C) and oxygen isotope (δ18O) data from gravity core SO264_55-1, which was recovered from Minnetonka Seamount (47°10.542 N 169°25.292 E) from 2936 m water depth. Measurements were performed on the benthic foraminiferal species Uvigerina spp., Cibicidoides wuellerstorfi, and Melonis barleanum. Sampling and analytical studies were carried out from 0.005–16.105 m core depth at ~2 cm spatial resolution. The isotope analyses were performed on a Thermo Scientific MAT 253 mass spectrometer with an automated Kiel IV carbonate preparation device.