While his predecessors had been embalmed after death, the Vatican claimed that Pope John Paul II was not embalmed and lay in state without normal treatment for preservation, which is evident by the grey colour taken on by the body. Also, it was customary for popes to have their organs removed after death.

While most modern popes undergo a form of preservation, Pope Pius XII (d. 1958) is famous for a disastrous attempt at "natural" embalming that effectively meant he was not preserved correctly. His physician, Dr. Galeazzi-Lisi, attempted an experimental method involving aromatic herbs and plastic wrap instead of traditional fluid exchange. This failed spectacularly; during the hot Roman summer, the body decomposed so rapidly that the Pope reportedly "exploded" inside his coffin during the procession, and guards had to be rotated frequently due to the overwhelming odor. Following this incident, the Vatican modernized its protocols. More recently, Pope John Paul II was not heavily embalmed in the traditional sense, though some light "hygienic preservation" was performed to allow for his lying-in-state. However, the most famous example of a non-embalmed pope in modern times is Pope Francis, who in 2024 updated his funeral rites to be much simpler, expressing a wish for a modest burial that avoids the elaborate, multi-layered preservation rituals of his predecessors.