Quintero made his first appearance of the season on 16 July, scoring once in a 2–0 win against Chiapas in the opening game of the 2016 Apertura. He would score again in América's next match, a 3–0 win over Venados F.C. in the Apertura 2016 Copa MX. Quintero picked up his first assist of the campaign on 23 July in a 3–1 victory against Toluca. On 6 August, he scored once and recorded two assists to help América to a 4–1 win over Veracruz. On 3 September, it was announced that Quintero was suffering from a thrombophlebitis in his right leg. The initial estimate was that he would be out for three to six months and miss the rest of the season. Quintero managed to return in time for the final match of the Apertura, recording two assists in a 3–3 draw with Pachuca on 19 November. During the first leg of the Liguilla quarterfinals, América and Guadalajara played to a 1–1 draw. Quintero would get an assist in the second leg to send "Las Águilas" through to the semifinals. After defeating Necaxa, América would face off with Tigres UANL in the final. Quintero came off the bench in the first leg, but did not feature in the second as Tigres won in extra time. At the 2016 FIFA Club World Cup, Quintero helped América defeat Jeonbuk Hyundai Motors in their first match before falling to Real Madrid in the semifinals. They would lose to Atlético Nacional on penalties in the third place game.