Despite the coronavirus pandemic, thousands of worshippers attended the historic event. Many of the people starting arriving at the mosque from the last night and several came early today.
"We see this as the second conquest of Istanbul," Selahattin Pamukcu, said, who came to witness the prayers.
Turkish President Recep Tayyip Erdogan also arrived in the mosque along with his wife. Erdogan was in the favour that the museum be converted into a mosque. On July 10, the country's highest court ordered that the world heritage site be turned into a mosque.
The day of the prayers is the 97th anniversary of the Treaty of Lausanne, which settled modern Turkey's borders following years of conflict with Greece and Western powers.
Erdogan, who has a nostalgia for the Ottoman empire, has called for the treaty's revision.
Erdogan, who seems to strengthen his nationalist credentials, has faced wrath from its NATO ally Greece, who see the reconversion as a provocation to the "entire civilised world".
"What is happening in (Istanbul) this day is not a show of force, but proof of weakness," Greek premier Kyriakos Mitsotakis in a statement said.