The Pope and the Turkish leader had a 50-minute meeting behind closed doors, during which they discussed the situation in Syria as well as refugees in the Middle East and the Trump administration's decision to recognise Jerusalem as Israel's capital, which they both oppose.
Officers in riot gear blocked around 150 protesters near Rome's Tiber River as Mr Edrogan paid the first Vatican visit by a Turkish head of state in 59 years.
Erdogan and the pope discussed the status of Jerusalem, which has always been regarded sacred by 3 religions.
The head of the Roman Catholic Church, Pope Francis, and the Turkish president on Monday condemned the U.S. decision to recognize Jerusalem as Israel's capital. The move was condemned and rejected by the Organization of Islamic Cooperation in the same month.
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Erdogan also expressed his gratitude for the welcome while the pope thanked the Turkish president for the official visit.
Back in December, Pope Francis called for the world to honor United Nations resolutions on Jerusalem: "I make a heartfelt appeal so that all commit themselves to respecting the status quo of the city, in conformity with the pertinent resolutions of the United Nations", he said.
On the eve of his departure Sunday, Erdogan said he planned to discuss the humanitarian situation in Syria, the battle against terrorism, Islamophobia, and the status of the city of Jerusalem.
The Vatican said Mr Erdogan and Francis also discussed Turkey's "reception of the many refugees and the challenges linked to this".
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Pope Francis, after leading a holy mass in St Peter's Basilica at the Vatican to mark the Feast of the Presentation of the Lord, on February 2, 2018. The Pope later hosted Chaldean Church leadership including Patriarch Sako. Francis met with him during his 2014 trip to Istanbul. The pontiff acknowledged a unsafe stereotype stigmatising Muslims was gaining ground.
The pope and Turkish president also exchanged gifts.
Following the private meeting the Pope gifted the President a bronze medallion, which shows an angel over the northern and southern hemispheres while a dragon tries to attack, Radio Free Europe said.
Aside from Erdoğan and his wife, the Turkish delegation included Foreign Minister Mevlüt Çavuşoğlu, Economy Minister Nihat Zeybekci and National Defense Minister Nurettin Canikli as well as EU Minister Ömer Çelik and Minister of Energy and Natural Resources Berat Albayrak. Rome also issued a 24-hour ban on demonstrations.
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