On 13 October 2011, Fink left the club to join Hamburger SV and on the same day Vogel was appointed as caretaker Manager.

[3] Vogel's first three games in charge of the team were the Swiss Cup fixture on 15 October, which ended in a 5–1 away win against FC Schötz,[4] the Champions League Group C fixture on 18 October 2011, a 0–2 home defeat against Benfica,[5] and the 1–0 away win in the Super League against FC Zürich.

[6] On 7 December 2011 he guided FC Basel to the round of 16 in the UEFA Champions League, defeating the 2011 runners up Manchester United by 2–1.

[7] After 11 games, four of which in the Champions League, with eight wins, two draws and only one defeat, it was announced on 12 December that Vogel had signed as head coach and manager.

[29] On 28 November 2022, he was announced as the new sporting director of his former club FC Basel in the Swiss Super League, per 1 January 2023.

[31] He coached the team for the remainder of the season and led them to the semi-final of the UEFA Europa Conference League, where they were eliminated in extra time by ACF Fiorentina, with a aggregate score of 3–4.

On 12 May, the club announced that Timo Schultz would take over as coach of the team for the next season,[32] thus allowing Vogel to return to his original position as sporting director.

[33] In his third stint as FC Basel manager, Vogel would merely last for one month: he was dismissed on 31 October 2023,[34] following four losses in a row with a goal difference of 0–10.