Zeidler started his coaching career with VfR Aalen in 2002 and was appointed manager of 1.

Following a one-year spell as manager of Stuttgarter Kickers, he spent three years as Ralf Rangnick's assistant at TSG 1899 Hoffenheim before joining French Ligue 2 side Tours as the head coach in 2011.

In 2012, he went on to FC Liefering, the second team of Red Bull Salzburg.

[1] On 3 December 2015, he was replaced by Thomas Letsch, who like Zeidler, also comes from FC Liefering.

On 3 June 2024, after six years at the helm of FC St. Gallen, he departed the club to take up the mantle at VfL Bochum.