After his retirement Duarte immediately began his coaching career, staying with his last club Leiria as assistant. In the tenth round of 2006–07's top division he was named coach of the first team, eventually helping it finish seventh.
In late 2007 Duarte left Leiria and, a couple of months later, was appointed manager of Burkina Faso. On 2 June of the following year, however, he was signed by France's Le Mans Union Club 72 on a two-year contract, while still working with the national team.
Duarte selected players to play for the Burkina Faso national team who he believed were eligible to play for the nation after they married Burkinabé women.Namibia complained about the fielding of Herve Xavier Zengue in two 2012 CAN qualifying games, stating that the player was not eligible under FIFA's statutes.