Calcareous nannofossils are micrometric calcite platelets secreted by the photosynthetic algae named coccolithophores and incertae sedis. Calcareous nannoplankton inhabit the photic zone from coast to open-ocean and have left an abundant fossil record since the Triassic. Therefore, they constitute an interesting material for geochemical studies although they have been overlooked in comparison to foraminifera. We have analyzed manganese distribution and valence in six calcareous nannofossil species representing different ages (Recent to Jurassic) and geological settings (land sections and deep ocean core-tops) and with different structures to assess the potential of Mn as a paleobiological or paleoenvironmental proxy. Nano x-Ray Fluorescence (xrf) maps were established at the esrf id22ni and id21 beamlines and Mn k-edge x-Ray Absorption Near Edge Structure (xanes) at id21. Mn is more abundant in nannofossils from pre-Quaternary rock samples than from core-top samples. In nannofossil rock samples, Mn nanoxrf maps show distributions correlated with primary crystalline organization whereas in nannofossil core-top samples, Mn is either absent or does not follow the crystal organization. Xanes analyses show that Mn is in the form of MnCO3. All these observations argue for Mn incorporation within calcareous nannofossils controlled by diagenesis through overgrowth of secondary calcite (Ca, Mn)CO3. Crusts grew along the original crystal growth directions. The incorporation of Mn in some core-top samples highlights potential early diagenesis input when the detached platelet lies on the seafloor or is still in the water column. Mn should therefore be considered a critical tool to identify diagenetic overgrowth rather than primary environmental conditions.