Sample preparation for Raman Microspectroscopic analysis of microbial cells mostly requires mounting of cells to Raman-inactive substrata such as mirror-finished stainless steel microscope slides. This can be achieved either by drying cell suspensions on stainless steel slides or by applying the Filter-Transfer-Freeze ("FTF") Technique (Taylor et al. 2017 protocols.io; dx.doi.org\/10.17504\/protocols.io.ikqccvw) when microbial cells have been collected on polycarbonate membrane filters before. Both techniques work very well for small and rigid prokaryotes. However, the compression forces and dehydration caused by the FTF-technique or by dry mounting results in considerable morphological distortions and collapsing of cells when applied to specimens of larger protists (e.g. ciliates). Therefore, we developed a sample preparation method that accommodates the delicateness of ciliates and allows Raman analysis of fully intact and hydrated cells under water through a water immersion objective lens. The protocol was established with the ciliate species Tetrahymena pyriformis and and enabled 3D-mapping of chemical fingerprints on a subcellular level during Raman scans of 12 hours and longer. This method might be applicable not only to protists, but with slight alterations to larger specimens or delicate tissues in general.