Mr. Appelbaum has dodged allegations of inappropriate sexual conduct for years, and was suspended for two weeks last spring because of accusations of harassment. In May, new revelations of sexual misconduct emerged, and Ms. Steele led a push for Mr. Appelbaum’s resignation. She said the Tor Project had been working with an independent investigator to look into the claims.

Mr. Appelbaum denied the accusations. In a statement last month, he said: “I want to be clear: The allegations of criminal sexual misconduct against me are entirely false.” His publicist did not respond to further requests for comment.

After the controversy, all seven of Tor’s board members agreed to give up their seats to make room for a new slate. In a joint statement on Wednesday, they said, “It is time that we pass the baton of board oversight as the Tor Project moves into its second decade of operations.”

The new board is part of Ms. Steele’s broader restructuring as she seeks to promote the legitimacy of the Tor Project. Apart from dealing with the allegations over Mr. Appelbaum, the organization has also struggled to fend off an image as a “Dark Web” tool used by drug dealers and pedophiles. An official from the Justice Department recently incorrectly cited a statistic claiming 80 percent of traffic on the Tor network involved child pornography. That statistic, however, came from a study involving a separate service, Tor Hidden Services, which accounts for less than 2 percent of all Tor traffic.

Since taking the Tor Project’s helm, Ms. Steele has replaced its directors of human resources and administration, moved the project’s base of operations to Seattle from Cambridge, Mass., recruited the new slate of directors, and searched for additional, alternative sources of funding.