The Manhattan district attorney’s office is expected to charge the Trump Organization and its chief financial officer with tax-related crimes on Thursday, people familiar with the matter said, which would mark the first criminal charges against the former president’s company since prosecutors began investigating it three years ago.

Any charges against the Trump Organization and Allen Weisselberg, the company’s longtime chief financial officer, would be a blow to former President Donald Trump, who has fended off multiple criminal and civil probes during and after his presidency. But the initial charges won’t implicate Mr. Trump himself, his lawyer said, falling short of an expectation built during a high-profile probe that included a battle over the former president’s tax returns that went twice to the U.S. Supreme Court.

The defendants are expected to appear in court on Thursday afternoon, the people said.

The Trump Organization and Mr. Weisselberg are expected to face charges related to allegedly evading taxes on fringe benefits, the people said. For months, the Manhattan district attorney’s office and New York state attorney general’s office have been investigating whether Mr. Weisselberg and other employees illegally avoided paying taxes on perks—such as cars, apartments and private-school tuition—that they received from the Trump Organization.

A sole focus on fringe benefits would be unusual, former prosecutors said. It is rare to charge an individual or company for failure to pay taxes on employee benefits alone, although such charges are used as part of larger cases.

The charges expected Thursday could be the first in a series of charges in the future, particularly if prosecutors are able to gain the cooperation of Mr. Weisselberg to bolster their broader investigation, former prosecutors said. Mr. Weisselberg has rejected prosecutors’ efforts to gain his cooperation, the people said.

The entrance to Trump Tower in Manhattan on Wednesday.

The entrance to Trump Tower in Manhattan on Wednesday.

Photo: angus mordant/Reuters

If prosecutors could show the Trump Organization and its executives systematically avoided paying taxes, they could file more serious charges alleging a scheme, lawyers said.

Mr. Weisselberg and his lawyers haven’t commented on the investigation or impending charges.

Mr. Trump has denied wrongdoing and said the investigations, conducted by offices led by Democrats, are politically motivated. Earlier this week, he said in a statement that the case is composed of “things that are standard practice throughout the U.S. business community, and in no way a crime.”

In recent virtual meetings, lawyers for Mr. Trump and his company tried to persuade prosecutors not to charge the Trump Organization, arguing that charging a company over fringe benefits or employee compensation was unheard of, The Wall Street Journal and others reported this week.

The tax-related investigation is part of a broader criminal probe into whether the Trump Organization and its officers overvalued and undervalued its assets on loan, tax and insurance documents for financial gain, the Journal has reported. The criminal probe, led by the Manhattan district attorney’s office, and civil probe, by the New York attorney general, have looked at financial dealing around some of the same properties, including Mr. Trump’s Seven Springs estate, in Westchester, N.Y., and the Trump International Hotel and Tower in Chicago, the Journal has reported.

The investigations by both offices remain open, and any charges filed Thursday wouldn’t preclude future action.

—Deanna Paul and Rebecca Ballhaus contributed to this article.

Write to Corinne Ramey at Corinne.Ramey@wsj.com