Troubles at the magazine surfaced in June, when the top editor resigned under pressure after staff members complained of a toxic culture.
The two staff members, Ryan Walker-Hartshorn and Jesse Sparks, gave notice weeks ago.
Walker-Hartshorn was the assistant to the editor in chief.
Sparks said he had accepted an offer to be an editor at Eater, a Vox Media food site.
“Jesse and Ryan were valued members of the team and we worked with them to address their concerns about former leadership at the brand,†a Condé Nast spokeswoman said in a statement.
“We very much wanted them to be part of the new team under a new editor in chief and offered them enhanced terms to stay through the transition.
The note, which Condé Nast shared with The New York Times, concluded that race had played no part in how team members were compensated.
After his departure, Roger Lynch, the Condé Nast chief executive, and Anna Wintour, the company’s artistic director and the chair of its diversity and inclusion council, met several times with Bon Appétit staff members
They pledged to diversify the staff, and their search for a new Bon Appétit editor in chief is ongoing