Weisselberg is accused, among other things, of withholding millions in taxes.
After being handcuffed into the courtroom, the 73-year-old Weisselberg denied the allegations.
Shortly afterwards, he was released on bail, but had to give up his passport.
Earlier in the day, Allen Weisselberg had voluntarily surrendered to the authorities.
Donald Trump is not being prosecuted.
But the current indictment is still a setback for the former Republican president.
Trump has previously called the investigation a politically motivated witch hunt.
The Trump Organization is a family business that owns golf clubs, hotels and luxury properties.
Just before Donald Trump took office in 2017, he handed over the management of the corporate group to his two eldest sons and to Allen Weisselberg.