The Miocene Climatic Optimum (MCO; ~16.9 to 14.7 Ma) provides an outstanding opportunity to investigate climate‐carbon cycle dynamics during a geologically recent interval of global warmth. We present benthic stable oxygen (δ18O) and carbon (δ13C) isotope records (5–12 kyr time resolution) spanning the late early to middle Miocene interval (18 to 13 Ma) at Integrated Ocean Drilling Program (IODP) Site U1335 (eastern equatorial Pacific Ocean). The U1335 stable isotope series track the onset and development of the MCO as well as the transitional climatic phase culminating with global cooling and expansion of the East Antarctic Ice Sheet at ~13.8 Ma. We integrate these new data with published stable isotope, geomagnetic polarity, and X‐ray fluorescence (XRF) scanner‐derived carbonate records from IODP Sites U1335, U1336, U1337, and U1338 on a consistent, astronomically tuned timescale. Benthic isotope and XRF scanner‐derived CaCO3 records depict prominent 100 kyr variability with 400 kyr cyclicity additionally imprinted on δ13C and CaCO3 records, pointing to a tight coupling between the marine carbon cycle and climate variations. Our intersite comparison further indicates that the lysocline behaved in highly dynamic manner throughout the MCO, with >75% carbonate loss occurring at paleodepths ranging from ~3.4 to ~4 km in the eastern equatorial Pacific Ocean. Carbonate dissolution maxima coincide with warm phases (δ18O minima) and δ13C decreases, implying that climate‐carbon cycle feedbacks fundamentally differed from the late Pleistocene glacial‐interglacial pattern, where dissolution maxima correspond to δ13C maxima and δ18O minima. Carbonate dissolution cycles during the MCO were, thus, more similar to Paleogene hyperthermal patterns.