On 11 July 2013, it was confirmed that Santa Cruz would stay with Málaga on a permanent three-year contract.
He was issued the number 9 shirt for the 2013–14 La Liga season following the departure of Javier Saviola.
Santa Cruz affirmed that he was happy to be staying at the club and the factor of family stability came into his decision as he was able to leave his children enrolled in the same school.
Santa Cruz first appearance of the season came in a 1–0 away defeat against Valencia on 17 August 2013.

Two weeks later, Santa Cruz scored his first league goal in a 2–2 away draw against Sevilla on 1 September 2013.

His first appearance in the 2013–14 Copa del Rey was in a 3–3 home draw against Osasuna on 8 December 2013.
Santa Cruz scored his last goal of the 2013–14 La Liga season in a 2–0 home victory against Villarreal on 21 April 2014.
He scored Málaga's first goal in the sixth minute of the match.
Santa Cruz concluded the season with six league goals as Málaga avoided relegation by six points.
On 11 July 2013, it was confirmed that Santa Cruz would stay with Málaga on a permanent three-year contract. He was issued the number 9 shirt for the 2013–14 La Liga season following the departure of Javier Saviola. Santa Cruz affirmed that he was happy to be staying at the club and the factor of family stability came into his decision as he was able to leave his children enrolled in the same school. Santa Cruz first appearance of the season came in a 1–0 away defeat against Valencia on 17 August 2013.
Two weeks later, Santa Cruz scored his first league goal in a 2–2 away draw against Sevilla on 1 September 2013.
His first appearance in the 2013–14 Copa del Rey was in a 3–3 home draw against Osasuna on 8 December 2013. Santa Cruz scored his last goal of the 2013–14 La Liga season in a 2–0 home victory against Villarreal on 21 April 2014. He scored Málaga's first goal in the sixth minute of the match. Santa Cruz concluded the season with six league goals as Málaga avoided relegation by six points.
Roque Santa Cruz