He started his head coaching career with Cibona from Croatia, where he won his first league championship in 2001.

He then worked with Krka Novo Mesto from Slovenia, Avtodor Saratov from Russia, Lietuvos rytas from Lithuania, Maccabi Tel Aviv from Israel, and Baskonia and Valencia from Spain.

[6] In August 2019, Spahija was hired by the Memphis Grizzlies, to be their assistant coach, where he spent the 2019–20 season.

[8] On 20 September, he signed as head coach of the Shanghai Sharks of the Chinese Basketball Association (CBA).

[9] Spahija led the senior Croatian national basketball team between 2001 and 2005, coaching them at the 2003 and 2005 European Championship tournaments.