The incident happened at the Compassion Centre in Ballymun at about midday on Sunday when around 40 people were gathered.
It's claimed a man wearing a balaclava and holding a shotgun, interrupted the service asking worshippers to take out their money and mobile phones. All members of the congregation were forced to lie on the ground.
Senior Pastor John Eniola described the incident as a "frightening experience". Recalling the events he said: "He put a gun to one of the members' heads, gave him a bag and told him to collect the money and phones. He did that and then he fled.
"It was frightening but we all stayed calm and did not struggle.
"Thankfully nobody was hurt. There was no fire."
Speaking about the gunman, he said: "We have never seen anything like that before but we pray for him, we forgive him and we would like to see him in church."
Local police are appealing for information - it's claimed the man got away in a stolen blue Fiat Panda.