Several hypotheses have been put forward to explain the onset of intensive glaciations on Greenland, Scandinavia, and North America during the Pliocene epoch between 3.6 and 2.7 million years ago (Ma). A decrease in atmospheric CO2 may have played a role during the onset of glaciations, but other tectonic and oceanic events occurring at the same time may have played a part as well. Here we present detailed atmospheric CO2 estimates from boron isotopes in planktic foraminifer shells spanning 4.6–2.0 Ma. Maximal Pliocene atmospheric CO2 estimates gradually declined from values around 410 μatm to early Pleistocene values of 300 μatm at 2.0 Ma. After the onset of large-scale ice sheets in the Northern Hemisphere, maximal pCO2 estimates were still at 2.5 Ma +90 μatm higher than values characteristic of the early Pleistocene interglacials. By contrast, Pliocene minimal atmospheric CO2 gradually decreased from 310 to 245 μatm at 3.2 Ma, coinciding with the start of transient glaciations on Greenland. Values characteristic of early Pleistocene glacial atmospheric CO2 of 200 μatm were abruptly reached after 2.7 Ma during the late Pliocene transition. This trend is consistent with the suggestion that ocean stratification and iron fertilization increased after 2.7 Ma in the North Pacific and Southern Ocean and may have led to increased glacial CO2 storage in the oceanic abyss after 2.7 Ma onward.