The largest church that has existed in Jerusalem is the Nea Church from 6th century, built by the Roman Emperor, Justinian. However, the church was destroyed in the course of time, and only after many centuries it was rediscovered. Today, only a small portion of the original structure in the form of a small fragment of the Southern Apse exists near the Dung Gate of Jerusalem and is visible to the public. Immediate to this structure is an archaeological park known as Gan HaTekumah, which displays remains from the Crusader and Arab periods. Remnants of the Northern Apse of Nea Church were also discovered, but they remain closed to the public, and it is much difficult to locate deep inside the Jewish Quarter of Jerusalem. See more in my previous post here.
Remains of the Northern Apse of the Nea Church