Dating back to the Spanish era, Bilibid Prison was actually about to be replaced by a new facility when the Japanese invaded. After briefly being used to intern Japanese and German citizens, the Japanese military has since used the facility to hold American POWs from Bataan as well as civilians overflowing from Santo Tomas.

The University of Santo Tomas had its main campus on the outskirts of the city, a facility that had since 1942 been in use by the Imperial Japanese Army as an internment camp.

The former headquarters of the US forces in the Philippines has been repurposed by the Japanese as the keystone of the defense of southern Manila.