As a player he spent most of his career playing for Croatian teams Varteks and Dinamo Zagreb before moving abroad and appearing for clubs in France, Denmark and Austria.
[1] In his international career, he played in French Stade de Vallauris, Danish Ikast FS (now called FC Midtjylland) and Austrian SV Casino Salzburg (now called FC Red Bull Salzburg) Besek started his coaching career in his hometown football club of Varteks as a player-coach within the Croatian 1998–99 Prva HNL league season.
He returned to another top-tier club with Slaven Belupo where in the 2001–02 Prva HNL he guided them to a respectable sixth[2] and reached the 3rd round of UEFA Intertoto Cup when the team lost against Aston Villa.
[3] This saw Varteks interested in his services again where within the 2002–03 Prva HNL campaign he aided them to an improved third at the end of the season and a runner-up place in the Croatian Football Cup.
At the end of 2015, Besek took over Birkirkara FC with which he achieved the highest result in then Maltese football club European history kicking Scottish Hearts out of the UEFA Europa League qualifiers.