In 2006, he had a short stint as a head coach in one of the greatest Lithuanian teams, Žalgiris Kaunas.

In June 2012, he became the head coach of the Ukrainian team Budivelnyk Kyiv.

On 1 July 2014, he signed a one-year contract to become the head coach of the Russian team Nizhny Novgorod.

On 18 June 2016, he signed a two-year contract to become an assistant coach of David Blatt's, with the Turkish club Darüşşafaka.

[3] On December 24, 2016, Bagatskis became the head coach of the Israeli club Maccabi Tel Aviv.