The original buildings, temples, mausoleums and the cathedral were destroyed by fire, natural disasters or air raids during World War II.

In 2015 a Treasure Gallery was opened on the underground level of the Daiden (great hall), and it currently houses paintings of Kanō Kazunobu and a model of the Taitoku-in Mausoleum.

"[4] Shūei (宗叡, 809-884), a disciple of Kūkai, founded a temple named Kōmyō-ji (光明寺) at Kaizuka (貝塚, present-day Kōjimachi in Chiyoda, Tokyo);[5] it is said to have been the forerunner of Zōjō-ji.

[9] At its peak the temple grounds had more than 120 buildings, but following the decline of Buddhism during the Meiji period (1868-1912), most of them burned during the Bombing of Tokyo in World War II.

[9] The 21 meter (69 foot) two-storied main gate, Sangedatsumon (三解脱門) was constructed in 1622,[9] and it is therefore the oldest wooden building in Tokyo.

If someone passes through the gate, he can free himself from three passions (貪 Ton; "greed", 瞋 Shin; "hatred", 癡 Chi; "foolishness").

[12] The Taitoku-in Mausoleum of Hidetada (and the monument to his wife Sūgen'in), Ienobu, and Ietsugu had been designated National Treasures of Japan, but were burned in World War II.

[15] Monthly events[9] Zōjō-ji was depicted multiple times in the art work of the Shin hanga artist Kawase Hasui during the 1920s and 30s.