The Vatican said in a statement that the pope had "accepted the resignation" of Archbishop of Ljubljana Anton Stres and the Archbishop of Maribor Marjan Turnsek.
Tiny Slovenia only has two Catholic archdioceses.
Both are leaving under canon law rules for a bishop "who because of illness or some other grave reason has become unsuited for the fulfilment of his office".
Slovenian media quoted by Italian news agency ANSA reported allegations that risky financial mismanagement by the two archbishops had left the archdiocese of Maribor bankrupt.