After one season with IK Gauthiod, Björkegren decided to leave and pursue an opportunity to manage a team at a higher level.

Björkegren and Linköping secured the title in the 2017 Damallsvenskan with two rounds to go,[7] despite losing Pernille Harder, Fridolina Rolfö, and Stina Blackstenius before the start of the season and selling its captain Magdalena Eriksson to Chelsea mid-season.

[8] Björkegren then led Linköpings FC to its best-ever position in the UEFA Women's Champions League, where he guided the team to the quarterfinals.

[13] Björkegren left Beijing BG Phoenix after the 2019 season to return to Europe for his family, noting upon his appointment to Apollon Ladies FC in June 2020 that he expected to become a father in August 2020.

[18] On 9 December 2021, it was announced that Björkegren would become the new head coach of Racing Louisville FC in the United States, which had completed its first season in the NWSL several weeks earlier.