Lewis' Continental Kitchen, in Bondi in Sydney's eastern suburbs, was targeted in a failed arson attack on October 15, 2024.
Five days later, it was hit again, causing extensive fire damage.
The alleged mastermind behind both attacks is Sayed Mohammed Moowasi, a 32-year-old member of the Nomads Outlaw Motorcycle Group.
He is accused of directing Wayne Dean Ogden, 41, and Juon Majok Mali Amuoi, 27, to commit the failed firebombing on October 15.
The two alleged accomplices are also accused of being involved in the attack on the deli five days later.
The trio was hit with fresh charges related to the alleged attempted arson when the cases came before Downing Centre Local Court on Tuesday.
In August, the Iranian ambassador was expelled from the country after revelations the regime had been behind the attack on the deli as well as the firebombing of the Adass Israel Synagogue in Melbourne.
Iran has denied the allegations.
Moosawi faces two charges of knowingly directing the activities of a criminal group over the separate arson of Curley Lewis Brewery at Bondi Beach on October 17, 2024 as well as the two attacks on Lewis' Continental Deli.
The 32-year-old also faces four charges of destroying or damaging property by fire.
The Carramar man is out on bail after putting up $2 million in security but did not appear at court on Tuesday.
He is barred from contacting Ogden, Amuoi, members of the Nomads gang, or any other witnesses in the case against him.
According to court documents, Amuoi took a sledgehammer to the called-off arson bid on October 15.
He remains on bail after appearing in court on Tuesday and did not speak to reporters after a brief hearing.
Ogden is accused of being the driver on both October 15 and 20 despite never holding a licence.
The 41-year-old First Nations man blackened his face for the earlier attempted attack and was behind a stolen BMW for the later successful firebombing, court documents allege.
None of the three men have entered pleas.
Their matters will next come before the court on February 17.
The fresh charges were laid weeks after a magistrate issued a stern warning to those seeking to commit crimes based on religious or racial hatred.
"This case is ... a reminder that anyone who intends to engage in racial or religious hatred like this, that they must and will be severely punished," said magistrate Scott Nash when sentencing anti-Semitic vandal Mohammed Farhat to prison in November.
Ten cars were graffitied, two were burned and four buildings vandalised in a 41-minute rampage in Woollahra, a heartland for Australia's Jewish community, in the dead of the night on November 20, 2024.
The 21-year-old was sentenced to one year and eight months behind bars with a non-parole period of 10 months.
Farhat - who has a Hezbollah flag tattooed on his neck - denied any racial motivations, saying he was directed from higher-up and acted because he had been promised cash or drugs.
While Mr Nash did not find Farhat's motivation proven beyond reasonable doubt, he noted senate hearings from March which showed individuals offshore used local criminals to leverage social cohesion concerns.
Farhat's accomplice 21-year-old Thomas Stojanovski has been sentenced to an 11-month intensive corrections order to be served in the community for his role in the vandalism.
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