After his appointment, Patriarch Nicephorus visited Al-Hakim at his capital in Egypt.
In the meantime, Patriarch Nicephorus continued rebuilding the Church of the Holy Sepulchre, which had been destroyed on Al-Hakim's orders in 1009.
In the re-building effort, Patriarch Nicephorus was helped by Joannichius, who would later succeed him.
However, in 1034, Jerusalem was hit by an earthquake that substantially damaged the city and the Church of the Holy Sepulchre.
In 1042, upon ascending to the throne of Constantinople, Emperor Constantine IX Monomachos finally funded the reconstruction of the Church, as well as other Christian establishments in the Holy Land, under the treaty concluded earlier by Ali az-Zahir and Emperor Romanus III.