In 1997, Nishino returned to Kashiwa Reysol and became a coach. In 1998, he became a manager. In 1999, he led the club to win the 1999 J.League Cup. In 2000, the club won the 3rd place in J.League Division 1 for 2 years in a row and he received Best Managers award. However, he was sacked in July 2001. In 2002, he signed with Gamba Osaka. In 2005, the club won J.League Division 1 for the first time in club history and he was elected for the Best Manager award. In 2008, the club won AFC Champions League and the 3rd place at Club World Cup. He was also elected AFC Coach of the Year awards. The club also won the 2007 J.League Cup, the 2008 and the 2009 Emperor's Cup. He resigned in 2011. In May 2012, he signed with Vissel Kobe as Masahiro Wada's successor. However, he was sacked in November. In 2014, he signed with Nagoya Grampus and managed the club until 2015.