[1][2] Skender started his managerial career at the age of 33, as manager of the second team of Osijek in the Croatian Third League.
[9] On 30 December 2023, Skender was announced as the new manager of Bosnian Premier League club Široki Brijeg.
[10] He debuted as manager in the Bosnian Cup second round on 11 February 2024, qualifying to the quarter-finals after a penalty shoot-out, following a 2–2 draw against Stupčanica Olovo.
[11] Following two more league victories against Sarajevo and Željezničar, Skender suffered his first defeat as Široki Brijeg manager on 2 March 2024, losing 1–0 away from home to Igman Konjic.
[13] On 12 May 2024, it was announced by Široki Brijeg that Skender had left the club by mutual consent, after the team's disappointing league campaign.