The midfielder returned to Bergamo this summer for an extension of the loan deal between La Dea and Napoli from last term.
"We had received some proposals and I am glad that Napoli and Atalanta found an agreement. One of my concerns was having to go to Napoli's training retreat knowing that I would not stay," the 26-year-old told L'Eco di Bergamo.
"Whilst an offer from Milan wasn't concrete, they had tried an approach. Whilst there were some tempting offers, I chose Atalanta because I owe them."