He recently called Turkey's killing of approximately 1.5 million Armenian Christians from 1915-1917 a genocide. Turkey has always strongly denied the claims of genocide during the time of the Ottoman Empire.
The pontiff's remarks have prompted the Grand Mufti of the Turkish capital Ankara, Professor Mefail Hizli, to say: "Frankly, I believe that the Pope's remarks will only accelerate the process for Hagia Sophia to be reopened for [Muslim] worship."
The cathedral of Hagia Sophia in Istanbul was originally built as a Christian place of worship in 537 BC, and was the seat of the Emperor Constantinople - the first Christian emperor - and the Patriarchate of Constantinople, which is branch of the Orthodox Church.
It became a mosque when the Ottoman Empire took over the city of Constantinople (now Istanbul) in 1453, and remained so until the state of modern Turkey was formed, which established the country as official secular. It made the mosque into a museum to symbolise this.
However there have been calls from some Muslims in Turkey for the Hagia Sophia to become a mosque, with secularists wanting to the building to remain a museum.
The first Quran reading in the Hagia Sophia for 85 years took place earlier this week, signalling intent from some Muslims to see the building back as a mosque.
Some believers also want the cathedral to revert back to a Christian place of worship, whilst secularists want the building to continue to be a museum free of religious practice.