St Michael's Orthodox church was packed with migrants from Eritrea, West Africa, who are left at the site following a clearance by French authorities.
French president Francois Hollande said that his country "cannot tolerate" the camps, describing them as "not worthy" of France.
Migrants living there have been gradually moved to different sites across the country before being processed and given the option to apply for asylum.
A small number of the 10,000 residents remain at the site.
The church is one of many hand-made structures - including mosques, schools and shops - that were built by the thousands who lived in the camp.
It is due to be demolished later this week but campaigners fear important artefacts and artwork inside will not be removed first.