According to interviews with a half dozen former and current employees, some of whom agreed to speak only on the condition of anonymity, Mari Ellen Loijens, the foundation’s top fund-raiser, routinely bullied and demeaned colleagues, made sexually and racially insensitive remarks and at times even threatened physical violence.

The employees say that Emmett Carson, the foundation’s chief executive, ignored multiple complaints about abusive behavior by Ms. Loijens because she was responsible for much of the organization’s growth.

“She brought in the money, made the place bigger, and he could go out and be a superstar,” said Rebecca Dupras, an executive who said she left the foundation last year because she no longer wanted to work with Ms. Loijens. “He could have stopped this and reined her in, and he didn’t.”

The Silicon Valley Community Foundation’s problems burst into view last month, when the Chronicle of Philanthropy published a detailed article outlining the allegations against Ms. Loijens. A day after the story was published, Ms. Loijens resigned.

Since then, Mr. Carson was placed on paid administrative leave, the head of human resources resigned and the law firm Boies Schiller Flexner was brought in to conduct an investigation. Mr. Carson is now negotiating his exit and will not return to the foundation, according to people familiar with the matter who were not authorized to speak publicly.