In 2006, Ruiz led Paraguay to its worst performance in a World Cup tournament by losing two games in the group stage, something that never happened in Paraguay's previous six presentations. He was heavily criticized by the press and fans because of his extremely defensive tactics used during the tournament, despite having young talent in offensive players such as Roque Santa Cruz, Nelson Valdez, Julio Dos Santos and Nelson Cuevas. Another point of criticism was his decision to bring several veteran players to anchor the team's defense.
He took over the 'CD Veracruz Tiburones' of Veracruz of the Mexican first division in 2007. In 2008 he is was named manager of one of the largest and most respected clubs in Ecuador, the Club Sport Emelec, but was fired on August 3, 2008 because of poor performance.