The CFA was called to the factory building on England Street in Dandenong South about 4.30am on Friday, taking 20 minutes to bring the blaze under control.
An arson chemist was called to investigate how the fire started.
News footage showed a burned-out car that had been smashed into a wall of the clubhouse.
Police would not confirm if the car is a line of inquiry.
Bikie members were seen at the site speaking to police.
No one was injured from the blaze, but police did save a little black kitten from the flames which was eventually taken to the vet.
The fire comes just two days after properties in the same region were raided by police.
Four people were arrested and drugs were seized when officers swooped on the four properties in Melbourne's southeast on Wednesday.