[1] Leaving the role after eleven months with Admira losing their first six games of the 2005-06 season,[2] and having moved through a series of Austrian men's clubs through the 2000s, Thalhammer made a switch to women's football in 2011.

With the U17s, Thalhammer achieved the first qualification of an Austrian women's national team for the finals of any European Championship, which took place in England in 2014.

After nine years as Austria women's coach, Thalhammer stepped down to return to the men's game for the 2020-2021 season with LASK Linz,[5] guiding the Upper Austrians to fourth-place, qualifying for the UEFA Europa League, and reaching the 2021 Cup Final, where they lost to Red Bull Salzburg.

Within two months, Thalhammer was approached by lowly Belgian Pro League team Cercle Brugge, who were second-from-bottom and fighting relegation.

[6][7] The Austrian won seven of his first eight games in charge at Cercle,[8] finishing the 2021-22 Pro League season 10th of the 18 clubs, missing out on the European play-offs by two places.