Upon his death, he was buried in the Church of the Holy Virgin (also known as Deir Al-Habash دير الحبش بمصر القديمة).
In his time, the Papal Residence was at the Church of The Holy Virgin Mary and St Mercurius in Haret Zuweila (حارة زويلة) in Coptic Cairo.
His time in the Patriarchate coincided with a series of Mamluke leaders (Sultans): Al-Malik (Sultan) an-Nasir Nasir ad-Din Muhammad ibn Qalawun (third time) (1309-1340) — (الملك الناصر ناصر الدين محمد بن قلاوون) — commonly known as an-Nasir Muhammad (الناصر محمد), or by his kunya: Abu al-Ma'ali (أبو المعالى) or as Ibn Qalawun (1285–1341).
Abu Bakr was imprisoned in the Upper Egyptian city of Qus, along with many of his brothers, and executed on Qawsun's orders two months later.
He became the 83rd Patriarch on 2 January 1340 AD, towards the end of the reign of Al-Sultan Al-Nasir ibn Qalawun (الملك الناصر ناصر الدين محمد بن قلاوون).
In one incidence, in May 1341, towards the end of the reign of Al-Sultan Al-Nasir, the Sultan banned the celebration known as the Feast of the Martyr that the Christians held annually on the 8th of Bashans (May) in the Shubra district.