[4] In 2006, Shamir was named the head coach of Hapoel Jerusalem, and signed a two-year contract.

[13] Shamir helped CSKA win the VTB United League title, and reach the 2014 Euroleague Final Four, where they eventually lost to his former team Maccabi Tel Aviv.

In 2014, Shamir was named the new head coach of Hapoel Eilat, signing a two-year deal.

[15] In the 2016–17 season, Shamir led Holon to the 2017 Israeli League Playoffs as the first seed, but they eventually were eliminated by Maccabi Haifa in the Quarterfinals.

On June 14, 2018, Shamir was named the Israeli Basketball Premier League Coach of the Year.

[17] In the 2018–19 season, Shamir led Holon to the 2019 Israeli League Playoffs and the 2019 FIBA Europe Cup Semifinals, where they eventually lost to Dinamo Sassari.

In July 2019, Shamir was appointed Director of Basketball at the New Zealand Breakers, joining them as head coach and in an off-the-court role.