On 18 January 2016, Djimsiti signed a three-and-a-half-year contract with Serie A side Atalanta, taking the vacant number 55 for the second part of 2015–16 season. He debuted on 3 May 2016 against Napoli in a 2–1 loss.
On 31 August 2016, Djimsiti was loaned out to Serie B side Avellino to gain more playing time.
On 21 May 2016, Djimsiti was named in Albania's preliminary 27-man squad for UEFA Euro 2016, but was left out of final 23-man UEFA Euro 2016 squad on 31 May.
He was returned to Albania national team by same coach Gianni De Biasi receiving a call up for the friendly match against Morocco on 31 August 2016 and the 2018 FIFA World Cup qualification opening match against Macedonia on 5 September 2016.