He spent most of his career with Primera División Argentina club Boca Juniors, but also had a brief spell with Spanish side Villarreal.

He played for five years at the club, when in the middle of the 2003–04 season, Villarreal CF of La Liga bought 50% of his contract for €2.8 million and acquired his services.

Villarreal was considered an excellent destination for Battaglia as there were already plenty of former Boca players such as Martín Palermo, Juan Román Riquelme, Diego Cagna, Rodolfo Arruabarrena and Fabricio Coloccini at the club.

Back at Boca Juniors he recaptured his old form and started to improve his game, becoming club captain and being called up to the Argentina national team in the World Cup Qualifiers match against Peru on 8 October 2005.

During the 'Torneo de Verano' of 2008, Battaglia scored in the Superclásico against arch rivals River Plate, in a game where which Boca Juniors won 2–0.

[8][9] In July 2021, Battaglia was named as an interim replacement for Boca Juniors manager Miguel Ángel Russo, who was in isolation together with the majority of the first team squad, after a defeat to Atletico Mineiro after a player had been tested positive.