After the 2008–09 season with 22 appearances for Ottl, he played less under new manager Louis van Gaal.
Following his fall out with Bayern manager Louis van Gaal, Bayern's President, Uli Hoeneß, stated on DSF Doppelpass that the player will be allowed to leave the club on a free transfer.
During the 2010–11 winter break, Bayern coach Louis van Gaal announced that Kraft would replace Hans-Jörg Butt as Bayern's first-choice 'keeper for the second half of the season.
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With the arrival of Louis van Gaal to Bayern, he began playing in centre midfield to accommodate wingers Arjen Robben and Franck Ribéry.