The Germany goalkeeper is joining Girona on-loan for the season. The decision arrives after Barca had pushed Ter Stegen to find himself a new club last summer.
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Despite claims of tension between Ter Stegen and Barca's top brass, Flick said on Saturday: "That's Marc's decision.
"He knows exactly what he wants. We have talked many times. I also talked to Deco (sporting director) about what can happen, but I have no further information.
"Even if Marc was loaned, he would still be our captain. He is one of the club's icons. That's his decision and we will accept it."