From 1998 to 1999, Engelbrektson organized a new joint training section within the Swedish Armed Forces Headquarters. He attended the Geneva Centre for Security Policy focusing on International Relations and Conflict Management from 1999 to 2000. He was then tasked to organize and lead a new international manning section within the Swedish Armed Forces Headquarters. In 2001, Engelbrektson was appointed deputy brigade commander of Gotland Regiment (P 18) and from December 2003 until June 2004 he was commander of the 9th Swedish battalion (KS09), part of Kosovo Force (KFOR), in Kosovo, where he experienced the mid-March fights in Čaglavica. He also served as deputy commander in the German EU Force Headquarters (FHQ) in Ulm, Germany. In June 2004, he was appointed acting commanding officer of Gotland Military District (MDG), a position he held until January 2005 when he was appointed Force Commander of the Nordic Battlegroup (NBG). Engelbrektson left that position in July 2008.