In December 1999 he agreed terms to join Deportivo La Coruña as a replacement for his compatriot Sergio Martínez,[2] and the move was officially completed the following January when he signed a five-and-a-half-year deal for an undisclosed fee, still remaining with Peñarol until the end of the season.

[3] Pandiani made his debut for the Spaniards on 27 August 2000, coming from the bench for Diego Tristán in a 2–0 win over Espanyol at Estadio Riazor in the Supercopa de España return match.

[14] In his first full season he scored only seven La Liga goals,[16] including a first-half hat-trick against eventual champions Real Madrid in the Santiago Bernabéu Stadium,[17] but was top scorer in the 2006–07 UEFA Cup with eleven as his club reached the final, which they lost on penalties to Sevilla.

[19] Scarcely used in his first year, he was instrumental for the Navarrese in the following campaign, especially after the arrival in mid-October of coach José Antonio Camacho,[20] finishing as the club's top scorer.

[21] On 30 January 2011, during half-time of a 1–0 home win against Real Madrid, he was involved in a "verbal spat" with Cristiano Ronaldo, suggesting afterwards that "As a footballer he is a phenomenon but to do the things he does, maybe he has a screw loose.

[27] In late August 2012, Pandiani signed a one-year contract with Segunda División club Villarreal, where his 18-year-old son Nico was a C-team player.

He said that although he had always wanted to coach, he still thought of himself as a player and was open to offers;[36] in June 2015, he signed for Lausanne-Sport of the Swiss Challenge League, with the remit of supervising and teaching the tricks of the trade to the 15-year-old striker Andi Zeqiri, who had already made his first-team debut.

[15] Despite his relatively successful career in Spain, Pandiani only received four caps for Uruguay,[40] the first coming on 28 March 2001 in a 1–0 home defeat against Paraguay in the 2002 World Cup qualifiers.

[46] Following a spell at Dibba Al-Hisn in the United Arab Emirates, where he signed his son Axel,[47] Pandiani was hired at Cerro in the Uruguayan Segunda División in June 2021.