The second attack on Saintfield Road Presbyterian Church in the south of the city happened at around 1am on Sunday, police said.
PSNI inspector Jonathan Francey appealed for anyone who may have noticed any suspicious activity around the church or anyone who has information about this incident to contact police.
Northern Ireland Secretary James Brokenshire said: "I am shocked and saddened to hear of the disgraceful attack on Saintfield Road Presbyterian Church and hall.
"My thoughts are with its parishioners who will be devastated by this news."
Northern Ireland First Minister and Christian, Arlene Foster, tweeted:
As I head out to church I am so sad to learn that Saintfield road Presb church has been attacked. Senseless hate crime
— Arlene Foster (@DUPleader) July 24, 2016
Church elder Alistair McCracken has said the congregation is unaware why they're being targeted.
Santfield Road said on their Facebook page on Sunday: "Due to a second arson attack of greater severity taking place in the early hours of Sunday morning, the entire church building and halls are strictly out of bounds.
"Please stay away from the church as investigations are still underway.
"Worship on Sunday morning WILL NOT go ahead at Saintfield Road, however, worship services are happening in the other local churches."
