In micropaleontological and paleoclimatological studies based on microfossil morphology and geochemistry, assessing the preservation state of fossils is of the highest importance, as diagenetic alteration invalidates textural features and compromises the correct interpretation of stable isotope and trace elemental analysis. In this paper, we present a novel non-invasive and label-free tomographic approach to reconstruct the three-dimensional architecture of microfossils with submicron resolution based on stimulated Raman scattering (SRS). Furthermore, this technique allows deciphering the three-dimensional (3D) distribution of the minerals within these fossils in a chemically sensitive manner. Our method, therefore, allows to identify microfossils, to chemically map their internal structure and eventually to determine their preservation state. We demonstrate the effectiveness of this method by analyzing several benthic and planktonic foraminifera, obtaining full 3D distributions of carbonate, iron oxide and porosity for each specimen. Subsequently, the preservation state of each microfossil can be assessed using these 3D compositional maps. The technique is highly sensitive, non-destructive, time-efficient and avoids the need for sample pretreatment. Therefore, its predestined application is the final check of the state of microfossils before applying subsequent geochemical analyses.