As a coach, he won the Austrian double, for the renamed Red Bull Salzburg, as well as the Swiss Super League with Young Boys.

Hütter decided to end his playing career in August 2007 due to a persistent Achilles tendon injury, and became assistant coach of the Red Bull Salzburg Juniors.

After ending his playing career in 2007, Hütter became assistant coach of Red Bull Salzburg Juniors.

He was appointed as the head coach of the Red Bull Juniors for the 2008–09 season, which he finished with a record of 13 wins, seven draws, and 15 losses.

[6] In July 2009, he became head coach of SCR Altach, which had just been relegated to the second division, with the goal of leading them back to the Bundesliga.

After a 0–2 loss to First Vienna FC on 3 April 2012, Hütter was sacked by Altach, as the club was of the opinion that a change in leadership was needed to secure promotion.

In April 2012, league rivals SV Grödig announced Hütter as head coach starting from 1 June 2012, replacing Heimo Pfeifenberger.

[25] On 18 August 2018, Eintracht Frankfurt were knocked out in the first round of the German Cup by fourth division team SSV Ulm.

On 13 April 2021, Hütter announced that he would leave Frankfurt using a buy-out clause and join Borussia Mönchengladbach for the 2021–22 season.

[36] A highlight of Hütter's one season came in the second round of the DFB-Pokal, where Mönchengladbach won 5–0 at home to Bayern Munich on 27 October 2021.

[37] On 4 July 2023, Hütter signed a two-year deal at Ligue 1 team Monaco, which had not qualified for a European competition in the previous season, succeeding Philippe Clement.

[39] He guided the club to a runner-up finish in the 2023–24 season, and qualification to the Champions League group stage for the first time since 2018–19.

[42] Hütter's grandmother persuaded his parents to name their son Adolf, in memory of his uncle, who died at the age of 27 in a rock avalanche.