The young centre-forward moved to Atalanta on Wednesday in a permanent transfer.
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La Dea have paid €25m up front with €3-4m in bonuses also part of the deal. Lecce have since announced they will retain a sell-on clause in the agreement.
The 25 year-old has signed a contract with Atalanta to 2030.
Meanwhile, Lecce paid tribute to Krstovic, stating through their media channels: "Determination, grit and goals: you gave everything for the Giallorossi shirt.
"Good luck, Nikola".