One congregation in Berlin has reportedly grown from 150 to more than 600 in just two years.
According to AP, Lutheran churches in Hannover and the Rhineland have also reported growing numbers of Iranians converting to Christianity.
At a baptism on Sunday, pastor Gottfried Martens from Berlin's evangelical Trinity Church asked one Iranian refugee Mohammed Ali Zonoobi: 'Will you break away from Satan and his evil deeds? 'Will you break away from Islam?'
To which he fervently replied: 'Yes.'
Martens then baptised him 'in the name of the Father, the Son and the Holy Ghost.'
Zonoobi, a carpenter from the Iranian city of Shiraz, arrived in Germany with his wife and two children five months ago.
Zonoobi said he had attended secret religious services in Iran ever since friends introduced him to the Bible at age 18. He decided to flee to Germany after several Christian friends were arrested for practicing their religion.
It has been suggested that some Muslims are converting in the hope of improving their chances of being granted asylum, despite no guarantees it could make a difference.
"I know there are, again and again, people coming here because they have some kind of hope regarding their asylum," Martens said.
"I am inviting them to join us because I know that whoever comes here will not be left unchanged."
German Chancellor Angela Merkel has insisted that Islam has a place in the country, which expects to spend around €6 billion to cope with some 800,000 migrants and refugees expected to have crossed into the country by the end of 2015.
For Zonoobi and his wife Afsaneh, who since her baptism goes by the name of Katarina, the christening marks a new beginning.
"Now we are free and can be ourselves," she said. "Most important, I am so happy that our children will have a good future here and can get a good education in Germany."