In early January 2009, he joined up with the team in Cancún for a training camp ahead of the 2009 Clausura season. He made his debut for Santos on 18 January 2009 in the first match of the Clausura, playing all 90 minutes in a 2–1 against Club América. Quintero started the first two matches of the season due to an injury to star Ecuadorian striker Christian Benítez. After he failed to score in his first 4 matches, there was some media criticism of his lack of goals, but was praised for his work rate. On 15 February Quintero scored his first goal for "Los Guerreros" in a 2–1 victory over Chivas. He made his first appearance in the CONCACAF Champions League on 25 February, coming on as a substitute in a 2–0 defeat to the Montreal Impact in the first leg of the quarterfinals. Quintero got his first assist for Santos on 1 March, finding Benítez outside the box, who then laced the ball into bottom right corner. Santos would go on to draw Club Necaxa 2–2. In the return leg of the CCL quarterfinals, Santos found themselves trailing the Impact 4–3 on aggregate as they entered stoppage time. Quintero slotted in a cross across the 6 yard box in the 91st minute to level the aggregate score at 4, however Santos still trailed on away goals. Quintero scored again in the 93rd minute to put "Los Guerreros" up 5–4 on aggregate and in to the semifinals. On 15 March, Quintero found the back of the net twice as Santos drew with Deportivo Toluca 2–2. He would stay hot in their next match, scoring twice to give Santos a 2–1 victory over Atlante in the first leg of the CCL semifinals. Quintero scored his 4th goal of the Clausura on 5 April to help rescue a 2–2 draw with Pachuca. In the second leg with Atlante, Quintero got an assist on Vicente Matías Vuoso's goal to put Santos up 3–2, however two late goals saw Atlante come back and advance to the final. Santos and Quintero failed to qualify for Liguilla. He enjoyed a solid debut season, scoring 8 and assisting 2 in 20 appearances across all competitions.