Skender started his managerial career at the age of 33, as manager of the second team of
Osijek in the
Croatian Third League. On 30 March 2019, following the departure of
Zoran Zekić, he was appointed manager of the first team. Skender was sacked by Osijek on 21 September 2019. On 19 June 2020, Skender became manager of
Slovenian PrvaLiga side
Olimpija Ljubljana. After finishing second in the first part of the
2020–21 season, he was sacked on 8 January 2021 along with all of his staff members. He was again appointed as manager of Olimpija on 12 October 2021, replacing
Savo Milošević. However, on 20 March 2022, he was sacked again without finishing the season, after a 1–1 home draw against
Domžale. On 30 December 2023, Skender was announced as the new manager of
Bosnian Premier League club
Široki Brijeg. 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. 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. He led the side to the
cup semi-finals, where they were knocked out 5–2 on aggregate by
Borac Banja Luka. 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. ==Managerial statistics==