The versatile midfielder was being paired with the Viola by some media outlets on Thursday, but the Nerazzurri insist it is just speculation.
“I have never spoken to Fiorentina about Bonaventura,” Atalanta director general Pierpaolo Marino told Radio Blu.
Bonaventura, 23, has scored seven goals in 29 games for the Bergamo club in Serie A so far this season.
The two teams will meet in the top flight on Saturday.
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