Cairnshill Methodist Church, off the Saintfield Road in Castlereagh, was broken into on Thursday night. The exact time of the attack is unclear.
A number of separate blazes were started and damage was caused to the interior of the building as a result.
Methodist superintendant, Rev Ruth Patterson said she could not understand why anyone would target the church.
"It's just totally random. We have very good community relations, very good relations with other churches and the local community."
The Rev Brian Anderson, president of the Methodist Church in Ireland, condemned the attack.
"At the heart of the Methodist identity is a saying by the Rev John Wesley in which he described Methodists as the friends of all and enemies of none.
"This has been at the heart of the Cairnshill Methodist congregation, whose only desire is to serve the community among whom it is set."
An historic stain glass window from an older church building was covered in soot but otherwise undamaged.
The main church room, where Sunday services are held, also escaped the worst of the damage.
Rev Anderson encouraged anyone with information to contact police.
A church has been damaged in an arson attack in south Belfast.