The Microsoft co-founder stepped back from the board as the software giants launched a probe into a two-decade-old affair.
A spokesperson for Mr Gates denied that his decision to leave the board had anything to do with the investigation.
On Monday, a spokesman for Microsoft said the software company had received a complaint in late 2019 that Mr Gates had “sought to initiate an intimate relationship” with a female employee in 2000.
“A committee of the board reviewed the concern, aided by an outside law firm, to conduct a thorough investigation,” he said.
“Throughout the investigation, Microsoft provided extensive support to the employee who raised the concern,” he said.
Mr Gates stepped down from the Microsoft board before the investigation managed to reach a conclusion.
A spokeswoman for Mr Gates acknowledged the affair took place when asked by the Wall Street Journal newspaper, but denied it had anything to do his decision to step back.
“There was an affair almost 20 years ago which ended amicably,” the spokeswoman said.
“Bill’s decision to transition off the board was in no way related to this matter. In fact, he had expressed an interest in spending more time on his philanthropy starting several years earlier.”
Mr Gates said that he took the decision so he could spend more time on his charity work with the Bill & Melinda Gates Foundation.
At the time, he wrote: “With respect to Microsoft, stepping down from the board in no way means stepping away from the company. Microsoft will always be an important part of my life’s work… I feel more optimistic than ever about the progress the company is making and how it can continue to benefit the world.”
In identical tweets, they said they had made the decision to end their marriage.
“We have raised three incredible children and built a foundation that works all over the world to enable all people to lead healthy, productive lives,” they said in a statement.
“We ask for space and privacy for our family as we begin to navigate this new life.”
Melinda, filed for divorce at a court in Washington state, saying “this marriage is irretrievably broken” when asked to explain the split and revealing there was no pre-nuptial agreement when they wed on a Hawaiian golf course in 1994.