Six fire engines and around 30 firefighters were called to the Church of the Ascension on Ascension Road in Salford after the blaze broke out at around 11.10pm on Sunday.
Bishop of Manchester Rt Rev David Walker wrote on Twitter: "Last night there was a devastating fire at the Church of the Ascension, Lower Broughton in Salford. Please pray for Fr David and the people."
Greater Manchester Fire and Rescue Service said no one was hurt in the blaze, which was not brought under control until the early hours of Monday morning.
Rushing to the church after noticing flames from his nearby home, fast food restaurant worker 17 year old Liam Cole said: "Initially I have seen a flash of orange light when I went to the bathroom.
"I ran outside realising it was really close and then I have seen it's my local church. Initially it wasn't that bad but all of a sudden it was engulfed in flames and the roof started falling through.
"There was a lot of ash and smoke from the roof going on the people standing very close."