The papal selection process began several weeks before the 4 November selection. About 2,400 clergymen and others shortlisted three candidates: Bishop Theodoros, Bishop Raphael, a former aide to the previous Pope, Pope Shenouda III, and Father Raphael Ava Mina, a monk in St. Mina's monastery near Alexandria, and the disciple of the [[List of Coptic Orthodox Popes of Alexandria|116th Pope]], Pope Cyril VI. The process faced controversy as many congregates sought a greater say in the process. The three were considered consensus candidates as they were not involved in church disputes and were neither too conservative nor too liberal.
The ceremony to choose the pope from the three consensus candidates was held at Cairo's
[[Saint Mark's Coptic Orthodox Cathedral, Cairo|St. Mark's Cathedral ]] at about noon and featured a marked police presence. Prior to the selection, Metropolitan Pachomius of Behira, [[locum tenens]] of the Church, sealed the chalice with the names with red wax and put it upon the altar as he led Mass. He then told the congregation: "We will pray that God will choose the good shepherd." Following a moment of silence, a blindfolded boy then picked Theodoros' name from the chalice. The thousands of congregates in attendance then erupted in ovation, tears or prayer. In reaction Theodoros II said, from the monastery at Wadi El-Natrun: "[We] will start by organising the house from within. It is a responsibility. Most important is...that the church, as an institution, serves the community." Egyptian President Mohamed Morsi congratulated Theodoros and called for Egyptian "unity" and "brotherly love" between Copts and the Muslim community.<ref name="ap"/>