Jerónima's remains were first buried in a niche within a wall inside the monastery, but her remains were later relocated five times. The first was in 1670 to deter local devotees, while the second happened in 1712 due to the reconstruction of the monastery, when the remains were placed in the lower choir. The third relocation was during the British Occupation of Manila in 1763, when her coffin was transferred to the old Church of Saint Francis in Intramuros. The remains were returned to the monastery in 1765, and later survived the aerial bombings during the Battle of Manila in 1945. In the 1950s, her bones were finally placed at the monastery's new site in Dilimán, Quezon City.