The charges are the first brought by New York prosecutors in the case since they launched their investigation nearly two years ago into the financial dealings of Trump, his company, his family, and associates.
Weisselberg and the company pleaded not guilty to criminal charges including grand larceny in the second degree as outlined in a lengthy indictment unsealed in Manhattan State Supreme Court. Weisselberg was released on his own recognizance but was required to surrender his passport.
"This was a 15-year-long tax fraud scheme," said Carey Dunn, general counsel for the Manhattan DA's office. "It was orchestrated by the most senior executives."
"During the operation of the scheme, the defendants arranged for Weisselberg to receive indirect employee compensation from the Trump Organization in the approximate amount of $1.76 million ... in ways that enabled the corporate defendants to avoid reporting it to the tax authorities," the indictment said.
The charges are a "disgrace" and "shameful," Trump told ABC News after the indictment was unsealed, calling Weisselberg "a tremendous person."
"Disgrace, disgrace, disgrace," the former president repeated.
The most serious charge against Weisselberg, grand larceny in the second degree, is a nonviolent felony that carries a maximum of 5 to 15 years behind bars. The most serious counts for the company are the criminal tax fraud charges, for which the company could be fined.
The indictment said that, beginning in 2005, Weisselberg used the Trump corporation's bank account to pay the rent for his apartment, and he and others paid his utility bills using the Trump corporation's account. The indictment also accuses Weisselberg of concealing "indirect compensation" by using payments from the Trump Organization to cover nearly $360,000 in upscale private school payments for his family, and nearly $200,000 in luxury car leases.
"Weisselberg intentionally caused the indirect compensation payments to be omitted from his personal tax returns, despite knowing that those payments represented taxable income and were treated as compensation by the Trump Corporation in internal records," said the indictment.
Trump has called the investigation a politically motivated "witch hunt" by Vance and New York Attorney General Letitia James, both Democrats. The investigation has been a joint effort by the DA's office and James, who campaigned on a promise of investigating the Trumps.
"The case brought by the New York District Attorney's Office is unprecedented," Trump attorney Alan Futerfas said in a statement. "We are unaware of any case brought by that office concerning employee compensation, and we cannot find any such case ever brought by the IRS. Compensation cases are resolved by civil tax authorities, not criminal charges."
"The CFO himself directed that company records be deleted to conceal his participation in the scheme," Dunn said during the court proceedings. "Even now, there's been no attempt to impose discipline on the people involved, to report the crimes, to repay the proceeds, or even to amend any of the false tax returns. Instead, when confronted by our investigation, the company, at the highest levels, decided not to accept responsibility and cooperate, which is what companies do if they want to be viewed as a good corporate citizen. Instead, it forced us into litigation for a year and a half, including two trips to the Supreme Court."
"Today is an important marker in the ongoing criminal investigation of the Trump Organization and its CFO, Allen Weisselberg," James said in a statement following the charges. "This investigation will continue, and we will follow the facts and the law wherever they may lead."
Two years in the making
For nearly two years the Trump case has been a focus of Manhattan prosecutors, who went all the way to the Supreme Court in the fight to access Trump's tax returns and financial records. The investigation stemmed from the testimony of former Trump attorney Michael Cohen, who told Congress the Trump Organization valued its holdings differently when seeking loans versus when talking to tax authorities.
After a Supreme Court ruling in March, documents were turned over to the Manhattan DA's office by the former president's accountants at Mazars USA. The Trump tax documents run into the millions of pages, a source told ABC News at the time. Around the same time, Vance's team expanded to bring on former federal prosecutor Mark Pomerantz to scrutinize the material and aid in building a case to present to a grand jury. Pomerantz, who was named a special assistant district attorney, has only worked on the Trump case since joining the Manhattan DA's team earlier this year. The former federal prosecutor specializes in white collar financial crimes.
In recent weeks, the Manhattan DA made the rare move of impaneling a special grand jury focused on the Trump probe. ABC News first reported that one of the most senior officials in the Trump Organization, Jeff McConney, was among several witnesses that appeared before the special grand jury. Sources familiar with the matter say no other members of the Trump Organization leadership were asked to testify.
Who is Weisselberg?
Weisselberg, who has worked for Trump for decades, is one of the longest-tenured Trump employees and has been described by Trump as one of the most loyal. Weisselberg worked for Trump's father, Fred Trump, before joining a young Donald Trump in building the Trump Organization.
Writing in his 2004 book, "Trump: Think Like a Billionaire," Trump described Weisselberg as someone who "knows how to get things done" and who did "whatever was necessary to protect the bottom line -- and refused to succumb to the pressures of risk."
Weisselberg also appeared in at least one episode of "The Apprentice," where Trump introduced him as "tough."
Days before taking the presidential oath of office in January 2017, Trump named Weisselberg, along with Trump's two adult sons, as trustees of the Trump Organization. Weisselberg's son, Barry, also works for the Trump Organization, where he has worked on some of the company's properties owned by the City of New York.
Weisselberg's former daughter-in-law, Jennifer Weisselberg, has been interviewed by the district attorney's office, she told ABC News, and was asked about everything from school tuition to the family apartment and several cars.
"Some of the questions that they were asking were regarding Allen's compensation at the apartment at Trump Place on Riverside Boulevard," Jennifer Weisselberg told ABC News in an interview earlier this year.
More outside Manhattan
In addition the Vance case, the Trump family and company are under civil scrutiny by the New York attorney general's office, which has deposed Weisselberg and at least one of Trump's children, Eric, regarding the company's financial dealings, including those of its two charitable foundations.
Additionally, the Washington, D.C., attorney general's office has had a yearslong probe into the 2017 Trump inauguration committee, investigating whether funds were properly spent and accounted for after Trump's inauguration raised the most money in history, with a total of $107 million.
Trump's other adult children, Donald Trump Jr. and Ivanka, have sat for depositions in that probe, as has Trump's longtime friend and inauguration chairman Tom Barrack. No charges have been brought in that case.
ABC News' Mike Levine and Luc Bruggeman contributed to this report.