In the 2015–16 season, he also managed the team of FC Red Bull Salzburg in the UEFA Youth League.

On 18 June 2017, Erzgebirge Aue appointed Letsch as their new manager, replacing the Schalke 04-bound Domenico Tedesco on a three-year contract.

[5] On 27 February 2018, he was appointed Austria Wien manager until the end of 2017–18 season, replacing Thorsten Fink.

The club went on to secure fourth place in the Eredivisie, reached the final of the Dutch Cup (which was lost 2–1 to AFC Ajax) and ensuring qualification for the UEFA Europa Conference League.

[10] On 18 December 2024, Letsch signed a contract to return to Red Bull Salzburg in Austria until the summer of 2027.