The cell size, degree of calcification and growth rates of coccolithophores impact their role in the carbon cycle and may also influence their adaptation to environmental change. Combining insights from culture experiments and the fossil record, we show that the selection for smaller cells over the past 15 Myr has been a common adaptive trait among different lineages. However, heavily calcified species maintained a more stable biogeochemical output than the ancestral lineage of E. huxleyi.