Coccolith dissolution together with post‐mortem morphological features are immensely important phenomena that can affect assemblage compositions, complicate taxonomic identification as well as provide valuable palaeoenvironmental insights. This study summarizes the effects of pH oscillations on post‐mortem coccolith morphologies and the abundances and compositions of calcareous nannoplankton assemblages in three distinct types of material—(i) Cretaceous chalk, (ii) Miocene marls, and (iii) late Holocene calcareous ooze. Two independent experimental runs within a semi‐enclosed system setting were realized to observe assemblage alterations. One experiment was realized with the presence of bacteria and, in contrast, the second one inhibited their potential effect on the studied system. The pH was gradually decreased within the range of 8.3–6.4 using a reaction of CO2 with H2O forming weak carbonic acid (H2CO3), thereby affecting [CO32−]. Further, a subsequent overgrowth study was carried out during spontaneous degassing accompanied by a gradual pH rise. The experiment revealed that the process and intensity of coccolith corrosion and subsequent overgrowth build‐ups are influenced by a plethora of different factors such as (i) pH and associated seawater chemistry, (ii) mineral composition of the sediment, (iii) the presence of coccoliths within a protective substrate (faecal pellets, pores, pits), and (iv) the presence/absence of bacteria. Nannoplankton assemblages with corroded coccoliths or with coccoliths with overgrowth build‐ups showed that the observed relative abundances of taxa experienced alteration from the original compositions. Additionally, extreme pH oscillations may result in enhanced morphological changes that make coccoliths unidentifiable structures, and might even evoke the absence of coccoliths in the fossil record.