During his two-decade rule, Erdogan has been widely criticised for converting ancient churches into mosques. He also made Islamic conservatism a leading social force in the country.
He has always countered his critics by maintaining that he was only restoring the rights of the pious Muslims in the staunchly secular republic founded by field marshal Mustafa Kemal Ataturk in 1923.
In 2019, Erdogan laid the first stone for the church's construction. It now will be a place of prayer for Istanbul's 17,000-strong Assyrian Christians.
"We are seeing big problems today across many parts of the world," Erdogan told the faithful as all-out war raged between Israel and the Palestinian militant Hamas in Gaza.
"But the solidarity shown here today -- I find it very important," Erdogan said.
"We always protect the oppressed against the oppressor. That is our duty."
Assyrian Christianity dates back to the first century AD, and community members once lived in a region stretching from southwestern Turkey to Syria and Iraq.
Its main church moved from the Turkish city of Mardin to Damascus in 1932. Some small Turkish churches have been quickly restored and reopened in the past century.
On Sunday, Erdogan said that 20 existing churches were repaired since his party came to power in 2002.
But the Mor Ephrem "is the first newly built church to open its doors since the founding of the Turkish Republic," Assyrian community leader Sait Susin told AFP by telephone.
In 2020, Erdogan drew international criticism and even indignation when he converted Instanbul's iconic Hagia Sophia, once the world's largest cathedral, from a museum into a mosque.
UNESCO had expressed "grave concern at the time.
But Erdogan did not budge and converted another church into a mosque the same year. The church, in this case, was Istanbul's Byzantine-era Chora church. After Erdogan's move, Greece called the conversion "yet another provocation against religious persons everywhere".
The new church, inaugurated by Erdogan, can accommodate 750 worshippers.
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