Flick joined the Bayern backroom team in the summer of 2019, initially as assistant to Niko Kovac, who was fired in November after a poor start to the season.
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The 55-year-old's arrival heralded a reversal in Bayern's fortunes, with the Bavarians four points clear in the Bundesliga table as they chase an eighth straight title.
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And he has now been rewarded with a contract that will keep him at the Allianz Arena for another two seasons.
Club CEO Karl-Heinz Rummenigge: "FC Bayern is very happy with Hansi Flick's work. The team has developed very well under him and plays attractive football, which is also reflected in the results. We are the only German club that is still represented in all three competitions.
"I also like the way he leads the team, his human qualities are convincing, his empathy speaks for him. FC Bayern trusts Hansi Flick and we are convinced that we will continue to achieve our goals with him in the future."
Flick himself added: "I look forward to tackling the upcoming tasks together with my coaching team and the team. The conversations with Karl-Heinz Rummenigge, Oliver Kahn and Hasan Salihamidzic were very good and characterized by great mutual trust.
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"Together we have defined the direction for the coming years. I am sure that we can achieve a lot together."
Prior to taking up his role at Bayern, Flick had worked with Germany boss Joachim Low between 2006 and 2014 and was part of the coaching set-up which was victorious in the 2014 World Cup.
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