After Indonesian President Suharto's fall from power in 1998, Ana Gomes was part of the diplomatic talks about East Timor between the Portuguese authorities led by Jaime Gama, and Indonesian authorities led by Ali Alatas. When it was decided Portugal would set up an Interests Section in Jakarta (with the Netherlands acting as protecting power), she was chosen to head it. In 2000, with the reestablishment of bilateral relations with Indonesia, Ana Gomes was the first Portuguese Ambassador in Jakarta, having played an important role both in the process leading up to the independence of East Timor and in the reestablishment of diplomatic relations between Portugal and Indonesia. According to ambassador Fernando de Oliveira Neves, as relayed in his work "O Negociador" (2019), Gomes showed "unusual professionalism" and had an "extraordinary role" in the negotiations, and became a friend of Ali Alatas who came to admire her.