The Belgian tactician, who resigned as Kenyan coach mid last month citing personal reasons, was confirmed by Guinea Football Association during a press conference held in Conakry on Friday.
The 61 year-old Belgian replaces Kanfory Sylla, who was sacked in January. Put was among more than 80 coaches who applied for the Guinea position.
The Guinea FA confirmed that Put, who is currently in Kenya, will sign a contract when he arrives in Conakry on Saturday.
The former Gambia and Burkina Faso coach quit the Kenyan job in a huff after his demands to have a backroom staff from abroad was turned down by FKF.
Put was appointed as Stars coach on November 18 last year during the FKF Annual General Meeting in Mombasa and led Kenya to the 2018 Cecafa Senior Challenge title after beating Zanzibar in the final.
His main task now is to help qualify the Syli National to the 2019 Africa Cup of Nations in Cameroon, and his first game in charge will be against Mauritania in a friendly set for Nouakchott on March 24.