Belemnites are valuable for reconstructing Jurassic and Cretaceous seawater temperatures, but their reliability hinges on the preservational quality of the fossil materials. Methods for assessing the preservational quality of fossils vary among studies. This research examined altered Cretaceous belemnites and seemingly well preserved Upper Jurassic belemnites from Tibet, aiming to evaluate established methods for differences between well preserved and altered fossil specimens. Results indicate that cathodoluminescence and the manganese content are particularly useful for detecting alterations, correlating strongly with the δ18O values. Elevated iron contents generally suggest alteration, though less reliable. Iron incorporation into the rostrum is not always connected to a change in δ18O value. Macroscopic features such as fractures, ventral invagination and apical line should be avoided in sampling. The colour of belemnite specimens can also serve as an indication of alteration, but is less reliable. Interestingly, the strontium content of belemnite rostra in our study negatively correlates with δ18O values, which contradicts most previous literature results. Finally, by disentangling patterns of diagenetic alteration and carefully correcting raw data for the effects of post-depositional alteration, it seems still possible to obtain useful carbon and oxygen isotopic data from fossil specimens that have suffered diagenetic alteration. Our conclusions are based on, and primarily apply to fossil materials from the Tibetan study area. However, fossils from neighbouring localities in India and Nepal show similar signatures, which shows that our observations are valuable for the broader Himalayan region and likely fossils that experienced similar orogenic processes elsewhere.