In 2003 Geovanni agreed on terms with Benfica and was signed on a free transfer, agreeing to a four-year deal, after an impressive spell with Benfica on loan from Barcelona. He scored his first goal for Benfica against Braga scoring a free kick. He was a mainstay in the Benfica starting line-up and was hugely involved in winning 3 trophies for Benfica, the Portuguese Cup, Portuguese League and Portuguese Super Cup. Moreover, he was named "Benfica Player of the Year" in 2004 and 2005.