The 56-year-old philanthropist has been working with lawyers at several firms since at least 2019 to unwind the marriage of more than 25 years, according to these people and the documents.

Last Monday, the billionaire couple announced they were ending their marriage. In a joint statement posted on Twitter, they said, “we no longer believe we can grow together as a couple in this next phase of our lives.”

The couple hasn’t said what prompted the split. One source of concern for Ms. Gates was her husband’s dealings with convicted sex offender Jeffrey Epstein, according to the people and a former employee of their charity, the Bill & Melinda Gates Foundation. Ms. Gates’s concerns about the relationship dated as far back as 2013, the former employee said.

The couple negotiated their divorce throughout the Covid-19 pandemic, the documents show. They have three children who are all now 18 years or older, the divorce filing shows. The youngest is a senior in high school.

According to the documents reviewed by the Journal, Ms. Gates and her advisers held a number of calls in October 2019 when the New York Times reported that Mr. Gates had met with Mr. Epstein on numerous occasions. Mr. Gates once stayed late into the night at Mr. Epstein’s Manhattan townhouse, the Times reported.

Bridgitt Arnold, a spokeswoman for Mr. Gates, said in 2019 that the software mogul and Mr. Epstein had met multiple times to discuss philanthropy. “

Bill Gates

regrets ever meeting with Epstein and recognizes it was an error in judgment to do so,” Ms. Arnold said at the time. Mr. Epstein died in jail in August 2019 awaiting trial on federal charges related to sex trafficking.

Ms. Gates, a global advocate for women and girls, had told her husband she was uncomfortable with Mr. Epstein after the couple met him together in 2013, the former employee of the Gates Foundation said. Mr. Gates and some employees of the Gates Foundation continued a relationship with Mr. Epstein despite her concerns, this person said.

The Daily Beast earlier reported on the 2013 meeting and Ms. Gates’s concerns with Mr. Epstein.

When asked about his relationship with Mr. Epstein in a September 2019 interview with The Wall Street Journal, Mr. Gates said: “I met him. I didn’t have any business relationship or friendship with him.”

A spokeswoman for Mr. Gates, who is 65 years old, said Friday he stands by his 2019 statement to the Journal and declined to comment further. A spokeswoman for Ms. Gates didn’t respond to questions about her reasons for seeking a divorce.

In early 2020, Mr. and Ms. Gates surprised many people when they said they wouldn’t attend the World Economic Forum in Davos, Switzerland, an annual gathering of business and world leaders that the power couple had attended for years.

A few months later, on March 13, Mr. Gates said he was resigning from the boards of

Microsoft Corp.

MSFT -2.48%

and

Berkshire Hathaway Inc.

BRK.B -0.31%

The Microsoft co-founder said he planned to focus more on his philanthropic efforts.

By that time, the Gateses were already in discussions to divide their vast wealth, according to the people familiar with the matter and the documents. Legal teams from both sides were privately in discussions with a mediator to work out a separation, the documents show.

Ms. Gates’s legal team by then already included New York divorce lawyer Robert Stephan Cohen, the documents show. Mr. Cohen has represented

Michael Bloomberg,

Henry Kravis

and

Ivana Trump

in their divorces.

Mr. Gates also has some star lawyers, including

Ronald Olson,

a partner at the firm Munger, Tolles & Olson LLP who has represented

Mark Zuckerberg,

among others. Mr. Olson is a board member at Berkshire Hathaway, where he sat alongside Mr. Gates and Mr. Gates’s close friend

Warren Buffett.

The May 3 divorce filing says the couple had agreed to a separation contract to divide their assets—a fortune estimated at $130 billion by Forbes. Their assets include a $131 million lakeside compound in Washington state called Xanadu 2.0, a rare Leonardo da Vinci notebook and investments in Microsoft and Four Seasons Hotels.

Last week, Mr. Gates’s investment firm transferred nearly $2.4 billion worth of public company shares to Ms. Gates, including stakes in car-dealership owner

AutoNation Inc.,

AN -3.17%

a Mexican broadcaster and a Canadian railroad.

The Gateses have said they would give away most of their wealth and donated more than $36 billion to the Gates Foundation over the years. The couple said they planned to remain co-chairs at the foundation and jointly lead it after their divorce. “We continue to share a belief in that mission,” they said in their

Twitter

statement.

Ms. Gates signed her divorce petition in Bellevue, Wash., near the family home and the foundation’s headquarters, according to the filing. Mr. Gates signed the papers from Palm Desert, Calif.

Write to Emily Glazer at emily.glazer@wsj.com and Khadeeja Safdar at khadeeja.safdar@wsj.com