Organic molecules preserved in fossils provide a wealth of new information about ancient life. The discovery of almost unaltered complex organic molecules in well-preserved fossils raise the question of how common such occurrences are in the fossil record, how to differentiate between endogenous and exogenous sources for the organic matter and what promotes such preservation. The aim of this study was the in-situ analysis of a well-preserved vertebrate fossil from 48 Ma Eocene sediments in the Messel pit, Germany for preservation of complex biomolecules. The fossil was characterized using a variety of techniques including time-of-flight secondary ion mass spectrometry (ToF-SIMS), scanning electron microscopy/energy dispersive x-ray spectroscopy (SEM/EDX), x-ray diffraction (XRD) and Raman spectroscopy. A suite of organic molecules was detected, including porphyrins, which given the context of the detected signal are most probably diagenetically altered heme originating from the fossil though a microbial contribution cannot be completely ruled out. Diagenetic changes to the porphyrin structure were observed that included the exchange of the central iron by nickel. Further analyses on the geochemistry of the fossil and surrounding sediments showed presence of pyrite and aluminosilicates, most likely clay. In addition, a carbonate and calcium phosphate dominated crust has formed around the fossil. This suggests that several different processes are involved in the preservation of the fossil and the organic molecules associated with it. Similar processes seem to have also been involved in preservation of heme in fossils from other localities.