Ardiles became coach of J. League Division 1 side Yokohama F. Marinos in January 2000, but was sacked in June 2001 following a poor start to the season. From 2003 to 2005 he coached Tokyo Verdy, with whom he won the 2004 Emperor's Cup, In July 2005 Ardiles was fired after a nine-game winless streak. In mid-2006 he moved to Israel to coach Beitar Jerusalem, from which he quit after only a few months in charge on 18 October 2006 due to severe differences of opinion with the club's board of directors. After a small break he was appointed Club Atlético Huracán manager in his native Argentina in September 2007, he steered the club to 7th in the table before resigning at the end of the Apertura 2007.