An ancient Egyptian crocodile mummy (MHNL 90001591, Musée des Confluences, Lyon, France) dating to the Roman period and discovered at Kom Ombo (Upper Egypt) was analysed through synchrotron multiscale microtomography. Using this advanced technology, the virtual autopsy of the animal was carried out without affecting the bones, flesh, balms and linen bandages. The technique allows for the precise analysis of the specimen's bones and tissue, enabling us to establish the cause of death and the last meal(s) of the animal. From these data, we can conclude that this crocodile was hunted while living in the wild. This is the first evidence for this mode of obtaining animals to produce mummies. With this case study, it is apparent that the praxis related to the mummification of animals in ancient Egypt are more diverse than the current Egyptological reconstruction of that phenomenon.