In a gesture designed to highlight his commitment to inter-faith dialogue, Pope Francis conducted a silent prayer alongside a senior Islamic cleric in Istanbul’s Blue Mosque on Saturday. Facing Mecca, Francis bowed his head in prayer for several minutes while standing next to Istanbul’s Grand Mufti Rahmi Yaran. The Vatican described the gesture as a “moment of silent adoration” of God.

Francis’s predecessor, Pope Benedict, caused dismay among many conservative Catholics and some Muslims when he appeared to pray in the same mosque on his visit to Turkey eight years ago. The Vatican felt compelled to publish a statement saying that Benedict had merely been in meditation, though he later acknowledged that he “certainly turned his thoughts to God”.

Francis then paid a visit to the Hagia Sophia, the most important cathedral of Orthodoxy for almost 1,000 years. The basilica was turned into an imperial mosque under the Ottomans when they conquered the city in 1453, and converted into a museum after the foundation of the Turkish republic in 1923.

His visit was followed by a papal mass in the Catholic Cathedral of the Holy Spirit, which the leader of the world’s 1.2 billion Roman Catholics said alongside Bartholomew I, head of the 300 million Orthodox believers worldwide.

At the entrance to the church, Turks and foreigners alike strained to catch a glimpse of the pope as he emerged after the mass. One Argentinian TV assistant director, who came to visit his Turkish girlfriend in Istanbul, said he was surprised and excited about the possibility to see the pope. “This is the first stop for me, I came straight from the airport,” he said.

Garbis Atmaca, 72, an Armenian jeweller from Istanbul, said he had high hopes for the pope’s visit. “It is very good that he came,” Atmaca said. “His visit will have a good impact on the Islamic world. It will help foster understanding and peace.”

The mixed Christian community in Turkey is very small, estimated at about 80,000 in a country of 75 million, and only the few Roman Catholics and Chaldeans regard the pope as their spiritual leader. Atmaca, who belongs to the Gregorian-Armenian church in Istanbul, said that he nevertheless holds the current pontiff in high regard. “He is a very modest man, the best pope we ever had.”

Three Austrian nuns who attended the mass said that they had never seen as much cheering for a pope. “We came to see Pope Benedict eight years ago,” one of them said. “But we have never seen anything like this.”

Francis’s visit comes at a time of extreme hardship for the dwindling Christian communities in the region, especially in neighbouring Syria and Iraq where Islamic State (Isis) militants have captured large swathes of land and persecuted Shia Muslims, Christians, Yazidis and others who do not agree with their radical interpretation of Sunni Islam. Many of those fleeing the violence currently live as refugees in Turkey.

The 77-year-old Argentinian pontiff urged that fundamentalism be fought not through military interventions, but by eradicating poverty, hunger and marginalisation around the world.

“Both [the pope and Bartholomew] are deeply concerned about the brutal treatment and expulsion of Christians from their homes in the region, which has historically been the cradle of Christianity,” John Chryssavgis, theological adviser at the Patriarch of Constantinople, said.

Some fear that increased authoritarianism, nationalism and President Erdogan’s constant focus on Sunni Muslim identity might lead to more pressure on minorities in Turkey, too; others believe the situation has started to improve for Christian minorities during the 12 years of Islamic Justice and Development party government.

“Things are good now, better than before certainly,” Atmaca said. “I think the Islamist rhetoric [of the government] is mostly show.”

Others feel there has been stagnation. “Things will likely not get worse under the AKP,” said Orhan Kemal Cengiz, a human rights lawyer and expert on minority rights. “But they will not get better either. The Christians in Turkey should stand up for their rights and make more demands.”

Speaking at the presidential palace on Saturday, Francis underlined the importance of religious freedom for everyone. “It is essential that all citizens – Muslim, Jewish and Christian – both in the provision and practice of the law, enjoy the same rights and respect the same duties,” he said in a joint press conference with Erdogan.

Later on Saturday, Bartholomew I, with whom the pope shares close personal ties, is to receive Francis at the ecumenical patriarchate.