Atmospheric pCO 2 is a critical component of the global carbon system and is considered to be the major control of Earth's past, present, and future climate. Accurate and precise reconstructions of its concentration through geological time are therefore crucial to our understanding of the Earth system. Ice core records document pCO 2 for the past 800 kyr, but at no point during this interval were CO2 levels higher than today. Interpretation of older pCO 2 has been hampered by discrepancies during some time intervals between two of the main ocean-based proxy methods used to reconstruct pCO 2 : the carbon isotope fractionation that occurs during photosynthesis as recorded by haptophyte biomarkers (alkenones) and the boron isotope composition (δ 11 B) of foraminifer shells. Here, we present alkenone and δ 11 B-based pCO 2 reconstructions generated from the same samples from the Pliocene and across a Pleistocene glacial- interglacial cycle at Ocean Drilling Program (ODP) Site 999. We find a muted response to pCO 2 in the alkenone record compared to contemporaneous ice core and δ 11 B records, suggesting caution in the interpretation of alkenone-based records at low pCO 2 levels. This is possibly caused by the physiology of CO2 uptake in the haptophytes. Our new understanding resolves some of the inconsistencies between the proxies and highlights that caution may be required when interpreting alkenone-based reconstructions of pCO 2 .