The 28-year-old actor, who has sparked fears over his mental health in recent months, could face a life-time ban from The Local Peasant in Sherman Oaks, California, after the manager witnessed him urinating in the car park during his four-hour visit to the eatery, reported TMZ.
"The manager followed Shia to the parking lot, where he saw the actor peeing on the wall ... Shia profusely apologised in an odd rant," a source said.
"Shia then went back inside and tried ordering food, but the manager had enough and told Shia to get out. The two of them had words, Shia paid his tab and stormed out vowing never to return," it added.
The alleged incident comes just weeks before the star was arrested at a Broadway theatre for yelling offensive language and slapping people's bottoms during a performance of 'Cabaret' at Studio 54 in New York City.
Shia was charged with harassment, disorderly conduct and criminal trespassing yesterday morning, and is set to appear in court on July 24.
Meanwhile, earlier this year, the 'Transformers' star stormed out of a 'Nymphomaniac' press conference in Berlin, before arriving on the red carpet for the film's German premiere wearing a paper bag on his head that read, 'I am not famous any more.'
He was also forced to apologise for alleged plagiarism and starred in his own silent art installation in Los Angeles.