Beukema joined Bologna in 2023 from AZ Alkmaar, and the 26-year-old made 80 appearances across all competitions for the Italian side over the past two seasons, including starting all eight games in their Champions League campaign last season.
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Napoli, who won their fourth Scudetto in May, have also added Belgian midfielder Kevin De Bruyne, Dutch winger Noa Lang and Italian striker Lorenzo Lucca to Antonio Conte's squad in the close season.