Marcelo joined Real Madrid during the January transfer window in 2007. On his arrival, Club President Ramón Calderón said, "He is an important signing for us. He is a young player who will inject some freshness into the side and is part of our plan to bring younger players into the squad. We're very happy because he's a pearl that half of Europe wanted." Many spectators hailed him as Roberto Carlos' potential successor in the left-back role.

Marcelo made his debut as a substitute in the 2-0 defeat against Deportivo La Coruña on January 7, 2007. On April 14, 2007, Marcelo made his first start for Real Madrid against Racing Santander, which Real Madrid lost 2-1. Under his new manager, Bernd Schuster, Marcelo had started nearly all of Madrid's league games. His ability, speed running across the field, attack, and defence had enabled him to become a very important player for Real Madrid.

After a string of poor performances Marcelo has found himself on the bench for much of the remaining season while under new manager Juande Ramos, mainly as deputy to Gabriel Heinze. Juande Ramos deployed Marcelo as a left winger on more than one occasion, and the Brazilian adapted well to his new role. He scored his first goal after receiving a heel flick from striker Higuaín and slotting the ball past the goalkeeper in Real Madrid's 4-0 thumping of Sporting Gijón. After the game, coach Juande Ramos declared that Marcelo's future would be positioned as a left winger, but will push back to defense when required. Marcelo scored his second goal for Real Madrid in their recent victory over Almeria, a powerful strike from outside of the box with his weaker right foot.

On April 18, 2009 he scored his third goal of his Real Madrid career, when he scored the only goal of the game against Recreativo Huelva away from home. He scored his fourth goal against Sevilla FC at Ramon Sanchez Pizuajin in April 2009.

Marcelo has been moved back to his left back position when the 2009-10 season started. With the departure of Heinze, he has received more playing time in the starting line up.