The Trump Organization and its financial chief have pleaded not guilty to criminal charges.
The company and its chief financial officer Allen Weisselberg are accused of defrauding tax authorities by awarding "off the books" benefits to executives.
The 15-count indictment laid by the Manhattan district attorney includes charges of tax fraud and falsifying business records as far back as 2005.
At the arraignment in Manhattan Criminal Court, prosecutor Carey Dunne described the scheme as "sweeping and audacious".
"It was orchestrated by the most senior executives who were financially benefiting themselves and the company, by getting secret pay raises at the expense of state and federal taxpayers," he said.
Weisselberg, 73, who has worked for the company for almost five decades and appeared at court in handcuffs, is accused of concealing $1.76m of income from tax authorities.
This included rent for a Manhattan apartment, tuition, and car lease payments.
Mr Trump denies any wrongdoing and has called the investigation a "witch hunt", accusing Democrat New York district attorney Cyrus Vance Jr and attorney general Letitia James of being politically motivated.
There is speculation that, although he is not personally charged in the case, it could hurt his hopes of a run for the presidency in 2024.
But Trump Organization lawyer Alan Futerfas said he was "very optimistic" the arraignment would not significantly hurt the business.
"If the name of this company was something else, I don't think these charges would have been brought," he said.
Weisselberg's lawyers, Mary Mulligan and Bryan Skarlatos, said before his court appearance that the executive would "fight these charges in court".
It is possible that the case against Weisselberg could give prosecutors the means to pressure him into cooperating with investigations into other aspects of the company's business, as he has extensive knowledge of Mr Trump's dealings.
The Trump Organization said Weisselberg was being used as "a pawn in a scorched-earth attempt to harm the former president", adding: "This is not justice, this is politics."
The Trump Organization operates hotels, resorts, and golf courses around the world - but before he became US president in 2017, Mr Trump put the firm into a trust overseen by his sons Don Jr and Eric, as well as Weisselberg.
Mr Trump's current role in the company is unclear.