On 31 August 2012, Santa Cruz returned to Spain and Andalusia, this time signing for Málaga on a season-long loan.
Santa Cruz was reunited with Argentine centre back and good friend Martín Demichelis, with whom he had played with at Bayern Munich.
His first league appearance for the 2012–13 season came in a 3–1 home victory against Levante on 16 September 2012.
Wearing the number 24, Santa Cruz was substituted onto the field in the 69th minute for Javier Saviola.
Two days later, Santa Cruz featured as a second-half substitute in Málaga's 3–0 Champions League home victory against Zenit Saint Petersburg on 18 September.
The encounter was his first UEFA Champions League competition return following several seasons, since the 2006–07 edition with Bayern Munich.

On 7 October 2012, Santa Cruz scored his first league goal for Málaga in a 2–1 away defeat against Atlético Madrid.
On 31 October, he scored a brace in a 4–3 away win against Cacereño in Malaga's first 2012–13 Copa del Rey fixture.

He scored his first league double in a 3–2 home victory against Real Madrid on 22 December 2012.
Santa Cruz had entered the field in the 65th minute of the match for Javier Saviola and netted both goals in the 73rd and 76th minutes of the fixture.
On 13 March 2013, Santa Cruz scored Málaga's second goal in their 2–0 Round of 16 UEFA Champions League home victory against Porto.
His goal gave Málaga a 2–1 aggregate scores and sent the club directly into the quarter-finals of the competition, where they would face Borussia Dortmund and be eliminated.
Santa Cruz had totaled eight league goals in 31 La Liga appearances as Málaga concluded in sixth position and qualified for the 2013–14 UEFA Europa League play-off round, however, the club was banned by UEFA from participating due to violations of UEFA Financial Fair Play Regulations.
On 31 August 2012, Santa Cruz returned to Spain and Andalusia, this time signing for Málaga on a season-long loan. Santa Cruz was reunited with Argentine centre back and good friend Martín Demichelis, with whom he had played with at Bayern Munich. His first league appearance for the 2012–13 season came in a 3–1 home victory against Levante on 16 September 2012. Wearing the number 24, Santa Cruz was substituted onto the field in the 69th minute for Javier Saviola. Two days later, Santa Cruz featured as a second-half substitute in Málaga's 3–0 Champions League home victory against Zenit Saint Petersburg on 18 September. The encounter was his first UEFA Champions League competition return following several seasons, since the 2006–07 edition with Bayern Munich.
On 7 October 2012, Santa Cruz scored his first league goal for Málaga in a 2–1 away defeat against Atlético Madrid. On 31 October, he scored a brace in a 4–3 away win against Cacereño in Malaga's first 2012–13 Copa del Rey fixture.
He scored his first league double in a 3–2 home victory against Real Madrid on 22 December 2012. Santa Cruz had entered the field in the 65th minute of the match for Javier Saviola and netted both goals in the 73rd and 76th minutes of the fixture. On 13 March 2013, Santa Cruz scored Málaga's second goal in their 2–0 Round of 16 UEFA Champions League home victory against Porto. His goal gave Málaga a 2–1 aggregate scores and sent the club directly into the quarter-finals of the competition, where they would face Borussia Dortmund and be eliminated. Santa Cruz had totaled eight league goals in 31 La Liga appearances as Málaga concluded in sixth position and qualified for the 2013–14 UEFA Europa League play-off round, however, the club was banned by UEFA from participating due to violations of UEFA Financial Fair Play Regulations.
Roque Santa Cruz