The former Germany striker has signed a one-year contract and will move into the role from July 1.
Flick’s current assistant Danny Rohl has extended his own deal until June 30, 2023.
“Hansi Flick and I have known each other very well since our years together with the German national team, we trust each other both professionally and personally,” said Klose, who has been coaching Bayern’s Under-17 side for the past two years.
“For me, this is the next step in my career as a coach. I hope that with my experience I can make an important contribution to Bayern achieving its sporting goals.”
Flick added: “With his experience as a former professional at the highest international level, Miro is the perfect addition to our team of trainers.
“We have known and esteemed each other for a long time and have had great success together with the national team. The fact that Danny Rohl will remain with us in the long term is also great news for my team and me.”
Klose, who retired in 2016, won two Bundesliga and DFB-Pokal doubles during four years with Bayern.
He won 137 caps and scored a record 71 goals in a distinguished Germany career, in which he reached the finals of the 2002 World Cup and Euro 2008, before winning the World Cup in 2014.
The winner of the Golden Shoe at the 2006 tournament on home soil, Klose is the leading goalscorer in World Cup finals history with 16.
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