WASHINGTON — Even as Donald Trump rose from New York real estate mogul to U.S. president, the innermost workings of his namesake real estate and branding company stayed shielded behind the black-tinted windows of his eponymous Fifth Avenue skyscraper.

Always run more like a family business than a blue-chip corporate empire, the private Trump Organization has operated free from the oversight of independent board members or pesky shareholders. But now that secrecy has cracked.

The plea agreement in federal court this week by Michael Cohen, who spent 10 years as executive vice president and special counsel at the Trump Organization and later served as Trump’s personal attorney, showed that federal prosecutors had excavated invoices, receipts, tax records, emails and other internal documents from Trump’s business.

Federal prosecutors also made clear their willingness to squeeze friends of the president. They reportedly got David Pecker, a longtime Trump ally who heads the company that publishes the National Enquirer tabloid, to provide evidence in the Cohen case in exchange for immunity from criminal charges.

Now the question is how much further they will dig into the murky business dealings and personal scandals at a carefully guarded company that remains key to Trump’s narrative of personal success despite years of bankruptcies, lawsuits and other controversies.

“The more you peel back, the more you’re likely to see irregularities that are worthy of investigation,” said Juan Zarate, a former Justice Department prosecutor who also helped pioneer tactics for tracking illicit cross-border financial transactions during the George W. Bush administration.

Two federal investigations pose the greatest threat so far. The U.S. attorney’s office in Manhattan is prosecuting the case against Cohen. Special counsel Robert S. Mueller III is looking into whether anyone from Trump’s campaign — which was based at Trump Tower — conspired with Russians to interfere in the 2016 election.

Trump suggested last year that he wouldn’t tolerate Mueller poking around in his business.

“I think that’s a violation,” Trump told the New York Times in an Oval Office interview. “My finances are extremely good, my company is an unbelievably successful company.”

Trump has repeatedly raised the idea of trying to shut down the Russia investigation by removing Mueller. Following through might be feasible if Trump were willing to pay the political cost. He would have less ability, however, to shut down the Cohen investigation since it would require moving against the large and well established U.S. attorney’s office in Manhattan.

Alan Garten, the Trump Organization’s top lawyer, said in a phone interview Thursday that “the company has been fully cooperative in the investigations.”

Trump has refused to release his tax returns to the public, and the company doesn’t disclose its annual revenue. But the perception of Trump as a titan of industry — forged in the popular imagination with the reality show “The Apprentice” — helped propel him to the White House, starting with his original announcement in the gilded lobby of Trump Tower.

“I’m really rich,” he said.

The Trump Organization has developed and run hotels, condominiums and golf courses around the country and overseas. Under lucrative licensing deals, Trump has also slapped his name — a name that’s “as hot as a pistol,” he’s said — on real estate developments, bottled water, steaks and vodka.

Some of those ventures failed or faded, and Trump endured a string of bankruptcies when he ran aground in the casino business in Atlantic City in the early 1990s.

His struggles to resuscitate his company after that could provide ample avenues for investigators if they choose to pursue them.

Trump found conventional sources of investment capital harder to tap, leading to suspicions — but no hard proof — that he turned to money laundering or other improper sources of funds. He and his company have never been charged with a financial crime.

Trump was also willing to cut deals and do business with shady characters. One example is Felix Sater, a convicted stock swindler who was a senior advisor to the future president. Sater maintained an office in Trump Tower, brought prospective deals to Trump’s personal attention and accompanied two of Trump’s adult children to Moscow in 2006 to look for business opportunities.

Prosecutors who want to unravel Trump’s array of businesses may find a willing partner in Cohen. His lawyer, Lanny Davis, said Cohen would cooperate with ongoing investigations, including Mueller’s.

“If they find evidence of criminality, based on Cohen’s information, that predates Trump’s presidency and has to do with his business and his business dealings, they’re going to go where the evidence takes them,” said Bradley D. Simon, a former federal prosecutor in New York.

Cohen pleaded guilty to eight counts of tax evasion, bank fraud and campaign finance violations in federal court in Manhattan on Tuesday. He specifically implicated Trump in his campaign finance violations, saying he had acted at the candidate’s direction in 2016 to pay a total of $280,000 to Karen McDougal, a former Playboy model, and Stormy Daniels, an adult film actress. Both said they had extramarital affairs with Trump.

Prosecutors said Cohen presented the Trump Organization accountant with a bank statement from Essential Consultants, a shell company incorporated in Delaware that he used to pay $130,000 to Daniels. He scrawled $50,000 for “tech services” at the top of the bank statement. Prosecutors said Cohen had solicited services “from a technology company during and in connection with the campaign.”

Company executives decided to pay Cohen double what he had asked to cover taxes, plus a $60,000 bonus, for a total of $420,000, according to the court filing. He arranged to get paid $35,000 a month for a year.

The arrangement created a sham paper trail in the Trump Organization. Cohen sent an invoice to an unnamed company executive in February 2017, seeking “payment for services rendered” for the first two months of 2017.

The executive forwarded it to a colleague for approval, and told someone else to list the payment to Cohen as his legal retainer. But the court filing noted Cohen had no retainer agreement, and the money was not for performing legal work.

During the court hearing Tuesday, Assistant U.S. Atty. Andrea Griswold said more documents — text messages, phone records and emails — would prove the campaign violations were undertaken “in coordination with the campaign or candidate for purposes of influencing the election.”

McDougal was paid $150,000 by selling the rights to her story to American Media Inc., which publishes the National Enquirer. The tabloid, which strongly supported Trump’s candidacy, never published the story, a practice known as “catch and kill.”

Pecker, chairman of American Media, agreed to assist investigators in exchange for immunity from prosecution, the Wall Street Journal reported Thursday.

Other members of the Trump Organization have also been connected to the payments.

In a recording that Cohen surreptitiously made before the election, he and Trump discussed how to buy the rights for McDougal’s story from Pecker to ensure the alleged sexual affair was not made public.

“I’ve spoken to Allen Weisselberg about how to set the whole thing up,” Cohen said, referring to the top bookkeeper at the Trump Organization. Trump interrupted: “So, what do we got to pay for this? One-fifty?”

Weisselberg was subpoenaed to testify before a grand jury in the Cohen investigation, the Wall Street Journal reported last month.

Using a corporate accountant to help pay hush money would raise eyebrows in most corporations. But at the Trump Organization, business and personal have been intertwined for years, raising the danger for the president now.

“At the end of the day, I work for the Trump family,” Garten, the company’s lawyer, told a legal trade publication in 2016. “That’s how I view my job. Whether it’s protecting their business interests or protecting their personal interests. I am here to assist them and represent them in any way they need.”

Trump’s children have held senior positions throughout the company, as his daughter Ivanka Trump and son-in-law, Jared Kushner, do at the White House.

During a 2011 deposition in a lawsuit involving a Florida project, Donald Trump Jr. said he wasn’t sure whether there was an organization chart for the Trump Organization.

“Could I make one? Yes,” he said. “Is there one officially? Not that I am aware of. But there could be.”

He added: “We kind of run a little bit like a mom-and-pop in that sense.”

chris.megerian@latimes.com

david.willman@latimes.com