A pronounced late Miocene cooling (LMC) from ~7 to 5.7 Ma has been documented in
extratropical and tropical sea surface temperature records, but to date, available proxy evidence has not
revealed a significant pCO2 decline over this event. Here, we provide a new, high‐resolution pCO2 proxy
record over the LMC based on alkenone carbon isotopic fractionation (εp) measured in sediments from the
South Atlantic at Ocean Drilling Program (ODP) Site 1088. We apply a recent proxy calibration derived
from a compilation of laboratory cultures, which more accurately reflects the proxy sensitivity to pCO2
changes during late Quaternary glacial‐interglacial cycles, together with new micropaleontological proxies
to reconstruct past variations in algal growth rate, an important secondary influence on the εp. Our
resulting pCO2 record suggests an approximately twofold to threefold decline over the LMC and confirms a
strong coupling between climate and pCO2 through the late Miocene. Within this long‐term trend are
pCO2 variations on sub‐myr timescales that may reflect 400‐kyr long‐eccentricity cycles, in which pCO2
minima coincide with several orbital‐scale maxima in published high‐resolution benthic δ18O records. These
may correspond to ephemeral glaciations, potentially in the Northern Hemisphere. Our temperature and
planktonic δ18O records from Site 1088 are consistent with substantial equatorward movement of Southern
Ocean frontal systems during the LMC. This suggests that potential feedbacks between cooling, ocean
circulation and deep ocean CO2 storage may warrant further investigation during the LMC