Jason Stevens, 41, surrendered to authorities Thursday morning and was charged with grand larceny and tax evasion for the alleged thefts between June 1, 2009, and Dec. 31, 2012, according to court papers.
He was released after posting $30,000 cash bail, according to the Brooklyn District Attorney's office.
Stevens shuttered his popular gastropub in DUMBO last Friday, leaving employees without weeks of pay, according to reports.
Dozens of brides- and grooms-to-be who planned to wed at the venue were also left in the lurch and out tens of thousands of dollars in wedding deposits.
The DA's investigation of Stevens was picking up steam just before the venue closed, sources said.
Stevens' next court appearance is scheduled for May 22.