The Habsburgs had an elaborate burial tradition: their hearts, intestines, and bodies were all buried in separate locations. When and how did this originate?

Hah, I'm actually taking a class right now that we talked about this at length. I'll do my best to answer your questions. I'll list my sources at the bottom.

This is a type of secondary burial and is fairly common. The Western tradition of burying someone and that's it is called primary burial. A lot of Native/Indigenous tribal communities practice secondary burials.

In specific regard to the Habsburgs, it was rather common for royalty to construct their own burial place or designate where they wanted to be buried and was attempted to be carried out as much as possible. However, bodies begin to rot very quickly after death and embalming practices weren't really a thing until much later. Embalming or maintaining the "wholeness" of a body after death could be done, but it was resource and material intensive and expensive. "Cremation had not only been explicitly forbidden under Charlemagne in the 8th century under the thread of the death penalty, but such destruction of the bones was also construed as destruction of the soul and thus the chance of resurrection. Burning the body was only used as a punishment." (Weiss-Krejci- 2001) So cremation wasn't really an option, even though an urn of ashes would have been MUCH easier to transport.

What developed is the body would be disemboweled, with soft tissue being removed and either buried or burned and then the cleaned remaining bones would then be transported to the final burial ground. This method was heavily disliked by the church and was banned a couple of times (1299 and 1300). This method is what happened to Babenberg Leopold VI (when he died returning from a crusade) in 1230, and again with Rudolph IV in 1365.

From the 11th c. onward, temporary storage of remains while they were "processed" was more and more of an option for those who could afford it (i.e. nobility and royalty). There were new monastic orders founded between the 11th c. and 13th c. that specifically dealt with basically death away from home or where the deceased wanted to be buried. The orders built new monastic buildings JUST for these types of deaths and were ceremonial and respectful holdings for people who died and couldn't be immediately transported. Again, with secondary burial, it is very common for the soft tissues to either be stripped or wait until they have decomposed and then the bones are collected and moved to a more permanent resting spot.

What became common with the Habsburgs is that because they were married off to all different corners of Europe, these halfway burial houses (for lack of a better term at the moment) would wait until there were several Habsburgs "ready for transport" and then a mass transport of bones would happen.

"For a large dynastic family that chooses a long-term burial place such as the Habsburgs and succeeding Bourbons at El Escorial, accumulation of bodies over time will create a space problem. This was overcome by the creation of additional mortuary chambers. Due to the construction of the Royal Pantheon under Philip IV in the 17th century and the Princes' Pantheon under Bourbon queen Isabel in the 19th century, of the 46 individuals in the sample that are buried at El Escorial at least 40 are secondary burials."

"CONCLUSIONS Of 868 people who died between 994 and 1993 three people were excarnated, one person was cremated (USA 1958) and two people were lost in a storm around Cape Horn in 1890. Corpses of 32 people were temporarily stored and saw later burial in a more or less excarnated state. In two thirds of the 32 cases the storage time ranged between six months and five years, but more extended periods were possible. Empress Anna was stored for 15 years and Emperor Frederick III (V) was moved into the large marble tomb at St Stephen's cathedral only 20 years after his death. At least 117 people were eviscerated and intestines and heart (rarely also brain, eyes, tongue or a finger) were buried into separate containers. Exhumation after the final funeral and relocation from one country, town, or building into another took place 95 times and involved 70 corpses. 392 relocations were carried out inside a building involving 247 corpses. Coffins were renewed 168 times (127 individuals) or opened 112 times (99 individuals). One may conclude that by archaeological definition at least 351 corpses (40.4%) have been tampered with. A more detailed investigation will most likely reveal an even higher percentage, since 200 cases (23%) could not be evaluated with certainty."

The article is REALLY interesting and I will happily share it if you'd like to read it (or anyone else who would like to read it).

Source:

Restless corpses: 'secondary burial' in the Babenberg and Habsburg Dynasties By: Weiss-Krejci, Estella. Antiquity , December 2001, Vol. 75 Issue 290, p769-780; 12p, Database: Biography Reference Bank (H.W. Wilson).

Edit: A few grammar errors corrected