Officers were called to The Islamic Centre in Newton Heath, Manchester, at about 01:20 BST.
Two men dressed in black were seen running from the scene, police said.
The fire was started just hours after two men ripped CCTV cameras from the Regent Street building's walls, at about 23:30 BST on Friday.
Police said the offenders were black men in black clothing with scarves covering their faces.
Insp Chris Hadfield, of Greater Manchester Police, said: "We believe the two incidents are linked and that the theft of the CCTV cameras was meant to help them carry out their arson attack on the minibus without being recorded.
"Fortunately there are several other cameras that capture the rear of The Islamic Centre, where the attack took place.
"We are investigating the possibility that this is a targeted hate crime."
Arsonists set fire to a minibus belonging to a Muslim community centre in what police say may have been a "targeted hate crime".