He fell to 5th in 2003 and then 7th in 2004. The following year, Nieto joined the Caracchi Ducati team for the 2005 Superbike World Championship. He only finished in the top 10 twice that season. He then rode for PSG-Kawasaki for two seasons. Nieto finished on the podium for his new team in race two of the 2006 season at Assen. In 2008 he joined Alsatre Suzuki and won his first world super bike race in the opening round in Qatar. He raced one more year with the team in 2009 after teammate Max Neukirchner was injured.