Three men have been found guilty of committing a terror act by burning a suburban Melbourne mosque.

A Supreme Court jury on Thursday returned the verdict for Abdullah Chaarani, Ahmed Mohmed and Hatim Moukhaiber who had stood trial charged with committing a terrorist act against the Imam Ali Islamic Centre at Fawkner.

The Islamic centre was was set on fire on December 11, 2016, in an attack that was partially caught on CCTV.

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Mohamed and Moukhaiber both denied any involvement and while Chaarani admitted he was there, argued he had been part of an act of protest, advocacy or dissent, and not terrorism.

During the trial, prosecutor Nicholas Robinson QC argued Chaarani's involvement was terrorism because the Shia mosque was targeted to intimidate Shia muslims.

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The prosecution told the court Chaarani and Mohamed tried to set fire to rugs and drapes with petrol on November 25, but the fire self-extinguished.

"They tried to set it on fire. They failed. So they came back two-and-a-bit weeks later armed with a lot more petrol and more things to make it burn," he said.

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