In November 2015 it was announced that Quintana would compete in the Tour de France, the Olympic road race and the Vuelta a España in 2016 and that he would start his season at the Tour de San Luis. He finished third in San Luis behind his brother, Dayer, who took the win. He went on to take the general classification at the Volta a Catalunya, becoming the third Colombian to win the race and the first to do so since Hernán Buenahora in 1998. Two weeks later, and struggling with the effects of illness, he finished 3rd in the overall classification of the Tour of the Basque Country.