During the season at
Maccabi Netanya, Atar was injured and decided to retire from his career as a player. He quickly signed as assistant coach at Maccabi Netanya, first alongside
Gili Landau and later on
Eli Cohen. At the end of the 2003–04 season, Cohen left the club, and Atar was chosen as the club's head-coach. Even though Netanya was relegated at the end of that season to the second league in Israel,
Liga Leumit, Atar remained in his position and helped the club return to the Premier League after one season. In 2006, Atar was sent home by Netanya's new manager,
Eyal Berkovich, and proceeded to move and coach
Maccabi Herzliya, from which he was fired after eight league games before returning to Netanya, later guiding the club to the second place in the Israeli Premier League, and the
UEFA Cup Qualifying rounds. Atar was later dismissed from Netanya, after team's owner
Daniel Jammer signed
Lothar Matthäus. In September 2008, he signed for
Beitar Jerusalem replacing
Itzhak Shum. Later that year he won the Israeli Cup, but was dismissed and replaced by Shum. On 29 September 2009, Atar returned once again to Maccabi Netanya, making it his third stint as the manager of the club. On 7 May 2011, he broke Netanya's undefeated streak from 1971 as he managed the team for 16 straight games without losing a match. On 23 April 2012, he signed a two-year contract for his home club of
Maccabi Haifa. In 13 November he was sacked from Haifa. On 19 March 2013, he returned to Maccabi Netanya for his fourth stint as the manager of the club. In the start of the 2014–15 season he worked as the manager of
Hapoel Haifa. He was fired after four months on the job. On 6 November 2015, Atar returned to Maccabi Netanya for his fifth stint as the manager of the club. ==Career statistics==