Skoubo's breakthrough came in the Danish Superliga club FC Midtjylland, when he scored 19 goals in 27 games during the 2001–02 season.

When German club Borussia Mönchengladbach wanted him in the team at the start of the next season, Skoubo made the switch.

Skoubo's club career in Borussia Mönchengladbach never took off and he was loaned out to English team West Bromwich Albion in January 2004.

[1] In Brøndby he regained his good form from his Midtjylland days, and Skoubo formed a good partnership with Swedish international Johan Elmander, Skoubo playing as the targetman and Elmander playing in a deep-lying role, which was successful in securing the Double for Brøndby, winning both the Danish Superliga championship as well as the Danish Cup.

At Roda, Skoubo had some impressive displays, and seems to form a perfect partnership with fellow Dane, Mads Junker.