The former Barca, Bayern Munich and Liverpool midfielder had a short spell alongside Flick last year, but was forced to cut short his stay due to visa issues.
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However, he has now joined Barca in a fulltime capacity, as the club announced on Thursday: "This is Thiago Alcántara's first official day of work as a member of the coaching staff.
"The former Blaugrana player began his work on the pitch today as a member of the first-team coaching staff, serving as assistant coach to Hansi Flick.
"His role will include, among other things, supporting tactical aspects and preparing training sessions, bringing his experience and vision to enrich the team's daily work."