The senior official at the center of sexual harassment allegations that have rocked one of the world’s biggest philanthropic organizations has resigned, marking a swift and dramatic downfall for a Silicon Valley fundraiser credited with helping to raise $8.3 billion.

Mari Ellen Loijens resigned Thursday from Silicon Valley Community Foundation, a day after a scathing report in the Chronicle of Philanthropy accused the nonprofit’s chief business, development and brand officer of routinely bullying her staff and making sexually inappropriate remarks.

Loijens has not responded to requests for comment. Despite her departure, questions continue to swirl around the foundation’s longtime president and chief executive, Emmett D. Carson, and his knowledge and handling of complaints about her.

Former employees quoted in the article and others said complaints about Loijens date back years and that Carson — a major force in the philanthropy world — was well aware of the concerns but did little to temper his star fundraiser.

Carson said in a statement that the foundation hired a law firm to investigate the claims about Loijens “immediately after learning of these recent allegations.”

“We do not tolerate inappropriate conduct of any kind at SVCF, and we investigate all claims of misconduct,” the statement said.

But the Philanthropy article quoted Rebecca Dupras, a former vice president for development, saying “it was well-known among all of SVCF leadership that Emmett did not entertain anyone complaining about Mari Ellen.”

“Anytime I tried to bring it up with Emmett, he immediately changed the subject,” Dupras said in the article. “As a CEO, he either knew or should have known. He should have asked questions, particularly as he saw the turnover in her division and saw the exit interviews from staff.”

In a Twitter post, Carson said: “I am deeply troubled and regret that former staff felt they could not report inappropriate behavior and urge any other staff to come forward. Listening and fixing this is Priority. 1.”

But that brought a rebuke from another former employee, Maria A. Moreno, who answered on Twitter: “Please stop acting like you did not know! I reported both you & Mari Ellen to HR July 2017. At the end of the day, I was the one who had to leave the foundation because it was a toxic work environment.”

Carson replied to her that he regretted she found the foundation a “difficult workplace. As you state, you brought your concerns forward and they were addressed with all concerned at the time. They were not hidden or ignored and you agreed your concerns had been fully addressed. I’m sorry you now feel differently.”

In an email, Carson also defended his response to complaints about Loijens, saying the nonprofit “immediately launched a third party independent investigation” by an outside law firm “upon hearing these allegations of sexual harassment for the first time, with the exception of a 2008 claim cited in the Chronicle of Philanthropy story, which was investigated at that time.”

The Philanthropy article, based on interviews with 19 former foundation employees, detailed several complaints about sexual harassment.

Dupras, a former vice president for development, said Loijens “made a lot of inappropriate comments about how people looked and how they dressed.” Another former employee, Elizabeth Dressel, said that while taking a new employee out after work, Loijens began “talking about vibrators.”

Lawyers specializing in sexual harassment cases said the foundation would be strictly liable if the harassment involved a supervisor rather than a co-worker. The company has an obligation under the law not only to deal with complaints, but also to make the harassment stop.