Some microorganisms, such as coccolithophores, produce an intricate exoskeleton made of inorganic solids. Coccoliths, the calcium carbonate scales of coccolithophores, are examples of the precise bioproduction of such complex 3D structures. However, the understanding of the cellular mechanisms that control mineral formation inside the cell, specifically the ability of these microalgae to transport high fluxes of inorganic building blocks, is still limited. Recently, using cryo‐electron and X‐ray microscopy, several intracellular compartments are shown to store high concentrations of calcium and phosphorous and are suggested to have a dominant role in the intracellular mineralization pathway. Here, live‐cell confocal microscopy and fluorescent markers are used to examine the dynamics of ion stores in coccolithophores. Using calcein and 4′,6‐diamidino‐2‐phenylindole (DAPI) as fluorescent proxies for calcium and polyphosphates, the experiments reveal an unexpected plethora of organelles with distinct fluorescent signatures over a wide range of strains and conditions. Surprisingly, the fluorescent labeling does not show changes along the calcification process and is similar between calcifying and noncalcifying cells, suggesting that these ion pools may not be a dynamic avenue for calcium transport. In such a case, the enigma behind the ability of coccolithophores to sustain intracellular calcification still awaits comprehensive elucidation.