Aboubakar began his career at Coton Sport and moved to Europe in 2010, playing for Ligue 1 clubs Valenciennes and Lorient, totalling 109 appearances and 26 goals in France's top division. In 2014, he signed for Porto, where he played 125 games and scored 58 goals, winning a Primeira Liga title. He won the Turkish Süper Lig while on loan at Beşiktaş in 2017, and again in 2021.
