In a lightning visit billed as an inspection, Erdogan took stock of the conversion work, the president's office said, providing pictures showing scaffolding inside the building.
Diyanet, the country's religious authority, said Christian icons would be curtained off and unlit "through appropriate means during prayer times".
It was unclear whether Erdogan planned to be among some 500 worshippers set to attend Friday prayers.
Turkey’s top court paved the way for the conversion in a decision to revoke the edifice’s museum status conferred nearly a century ago.
The sixth-century building had been open to all visitors, regardless of their faith, since its inauguration as a museum in 1935.
Earlier this week, Diyanet said the building would continue to be open to all visitors outside the hours given over to prayer.
The UNESCO World Heritage site was built as a cathedral during the Byzantine empire but converted into a mosque after the Ottoman conquest of Constantinople in 1453.
It was designated a museum in a key reform of the post-Ottoman authorities under the modern republic’s founder Mustafa Kemal Ataturk.
Erdogan said last year it had been a "very big mistake” to convert the Hagia Sofia into a museum.
The reconversion sparked anger among Christians and tensions between historic foes and uneasy NATO allies Turkey and Greece.