Marine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO
2
) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO
2
Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone
ɛ
p
record, we propose that decreasing CO
2
partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO
2
, suggesting an additional regulator of calcification such as alkalinity.
The impact of future and past carbonate chemistry changes on calcifying plankton is poorly understood. Here, the authors show that coccolithophore degree of calcification decreased significantly between 6 and 4 million years ago, in line with declining aqueous CO
2
concentrations.