The pontiff touched down in the ancient city from nearby Erbil on Sunday to embark on the third day of his stay. The 84-year-old was able to witness the first-hand destruction caused by war in the former Islamic State stronghold.
He was given a guided tour of the ruins of the Syriac Catholic Church and later led prayers.
Pictures show the Pope sitting in the front of a golf buggy, without a face mask, as he was escorted around places of worship and homes destroyed by years of fighting.
The head of the Catholic Church has already received his coronavirus vaccine and was surrounded by Vatican aides who are all wearing a face covering.
Pope Francis is the first papal visit to Iraq and is seen standing in the middle of the outdoor square speaking with faith leaders and worshippers – again without a face mask.
Later, he appeared moved by the damaged caused to once-thriving region and prayed for all those who had lost their lives.
Pope Francis said: “How cruel it is that this country, the cradle of civilization, should have been afflicted by so barbarous a blow, with ancient places of worship destroyed and many thousands of people Muslims, Christians, Yazidis and others forcibly displaced or killed.
“Today, however, we reaffirm our conviction that fraternity is more durable than fratricide, that hope is more powerful than hatred, that peace more powerful than war.”
He added hope could never be “silenced by the blood spilled by those who pervert the name of God to pursue paths of destruction”.
The northern city was occupied by Islamic State from 2014 to 2017.
The extremist group lead a barbaric regime and persecuted Christians and Muslims who opposed them.
Over the past two decades, the Christian population in Iraq has dropped to just 300,000 from highs of 1.5 million in 2003.
Father Raid Adel Kallo, pastor of the destroyed Church of the Annunciation, said he left in 2014 with 500 Christian families and revealed fewer than 70 families are present in the region now.
The four-day trip began on Friday and Vatican officials had privately urged the Pope against the visit due to security concerns – but he could not be dissuaded.
Pope Francis said it was important to make the trip even if minority Christians in Iraq only saw him on TV.
Baghdad has been at the centre of increased violence and last month rockets hit the city’s fortified Green Zone – the location of government buildings and foreign embassies.
In January, a double suicide attack killed at least 32 people in Baghdad.
Prior to the trip Archbishop Bashar Warda of Erbil said the Pope would be accompanied by up to 10,000 security personnel.