Hawzah News Agency (Manchester, UK) - Crews found the ground floor alight and spent several hours battling to put out the flames.
Al-Falah is in the middle of being refurbished and the fire destroyed building materials, windows, part of the ceiling and a carpet that had only recently installed.
Imam Mazz Mahwd, 24, said the mosque was largely empty at the time and no one was hurt.
"I was upstairs and someone came and said 'there's smoke'," he said.
"I came down and the smoke was everywhere, the fire was quite big. I called the fire service and they came and did an amazing job.
"They were through in a flash. They think someone threw something that started the fire, I don't what."
"I didn't see or hear anything, but residents said they saw two or three guys run off."
Mr Mahwd has only recently joined Al-Falah and said he has found the mosque to have a positive relationship with the Cheetham Hill community.
But some worshippers, who have attended for decades, say it has been plagued by anti-social behaviour.
One taxi driver said his car windows have been smashed several times.
He said the problems were even worse when Al-Falah was based directly across the road in the former Apollo pub.
"People weren't happy when it became a mosque," the taxi driver said.
Al-Falah moved to its new location around five years ago and Mr Mahwd said it needs more protection from police and the council.
It is understood a particular point of contention is getting metal grills and fencing put up around the building.
"We're concerned about general security," said Mr Mahwd.
"This is a place of worship and it's needs to be secure."
Another worshipper who came to the scene to see the damage was left furious.
"I'm not happy about this at all," he told the Manchester Evening News examining charred windows and carpet.
"I get on with all the community and this just isn't right."
Mr Mahwd said the mosque has a large congregation and he expects they will help with fundraising to get repairs sorted quickly.
"We have four or five hundred people in the downstairs prayer hall on a Friday night, and maybe half of that upstairs," he said.
"Whenever we ask for a donation for anything, people want to help straight away so I don't think it will be a problem.
"We don't want this to be a negative."
A spokeswoman for Greater Manchester Fire and Rescue Service said crews believe the fire was started deliberately.
She said: "At 10.31pm on December 9, 2018, GMFRS were called to a building fire at a commercial property on Heywood Street in Manchester.
"Three fire engines from Manchester Central and Broughton attended. Fire involved some building materials on the ground floor and measured approximately 25 metres by 25 metres.
"Firefighters used hoses and breathing apparatus to extinguish the fire and were engaged at the scene for approximately two hours and ten minutes. Fire is suspected to have been started deliberately and police are investigating."
Police are also investigating.
A spokeswoman for GMP said: "Shortly after 10.45pm on Sunday 09 December 2018 police were called by Greater Manchester Fire and Rescue Service to reports of a fire at a Mosque on Heywood Street, Cheetham Hill.
"Enquiries into the full circumstances around this incident are ongoing."