On 28 May 2021, Gustafsson was named the new manager of Croatian Prva HNL side Hajduk Split.[1] He signed a two-year contract, with the option of extending for a further one year.[2] Gustafsson arrived at Hajduk after holding the position as manager for four and a half years at Allsvenskan club IFK Norrköping.[3]
Gustafsson rejoined the Swedish national under-21 team at the beginning of 2022. On 9 May 2022, it was announced his contract had been bought out by Polish club Pogoń Szczecin, and he replaced Kosta Runjaić as team manager at the start of the 2022–23 season.[4] In charge of Pogoń in 87 official matches, Gustafsson led the club to back-to-back fourth-place finishes in the league, as well as the 2023–24 Polish Cup final. On 15 August 2024, Pogoń announced they have agreed to part ways with Gustafsson after he accepted an offer from an unnamed Saudi Pro League club.[5]
On 22 August 2024, Gustafsson was appointed as manager of Saudi Arabian club Al-Fateh.[6]