At the beginning of the 2007–08 season, he returned to Atalanta for € 1.9 million [3] when the club bought back half of his registration rights from Vicenza (€1M cash plus Brivio).

[3] The overall transaction means Vicenza paid Atalanta €100,000 cash in net, plus Padoin, to acquire Brivio and Zampagna outright.

On 22 December 2014, in the 2014 Supercoppa Italiana final against Napoli in Doha, Padoin came on as a substitute for Stephan Lichtsteiner after 79 minutes.

In the resulting penalty shootout, which went to sudden death, he had the decisive spot-kick saved by Rafael, handing Napoli the victory.

[12] Padoin has been praised by his managers for his work-rate, consistency, tactical intelligence, and versatility, as he is capable of playing in several positions, and adapting himself to different formations.