In July 2017, Fontes took command of Combined Security Transition Command – Afghanistan, replacing Richard Kaiser. Concurrently, she also serves as a deputy chief of staff in charge of security assistance for the Resolute Support Mission. Fontes is the highest-ranking female military officer in Afghanistan since the American invasion of that country in 2001. Asked in November 2017 about her assignment, Fontes replied to "Stars and Stripes" that she hoped the public would judge her performance as an Army officer regardless of her gender. Despite the flood of negative comments "Stars and Stripes" reported they received in response to her appointment to CSTC-A, Fontes stated that she was not surprised. She said "if I worried about that, I wouldn't have time to do anything else."