The 26-year-old has a £44m release clause in his contract at the Wanda Metropolitano, and Spanish journalist Guillem Balague has said, via his Youtube channel, that the midfielder is refusing to sign a new deal.
The Ghana international could be a big-money arrival at the Emirates Stadium this summer, although Mikel Arteta's side are seemingly facing a battle to keep hold of their captain.
Indeed, Pierre-Emerick Aubameyang's contract with the London giants is due to expire in June 2021, and it is thought that he could depart ahead of the 2020-21 campaign.
Here, Sports Mole looks at how Arsenal could line up next season if Thomas arrives from Atletico and Aubameyang leaves in search of pastures new.
There is no question that Partey's arrival would boost Arsenal's midfield, and it would not be a surprise to see the Ghana international line up alongside Granit Xhaka if he does indeed make the move this summer.
Xhaka's career at the Emirates Stadium looked over under Unai Emery, but Arteta is a big fan of the Switzerland international, who now looks set to remain in the English capital.
Partey has only scored 15 times in 174 appearances for Atletico but his energy, work-rate, athleticism and defensive capabilities would bring a lot to the team next season.
Saka's own future at the club is the subject of speculation as he has not yet extended his deal which expires next summer, but the 18-year-old has made 29 appearances during a successful 2019-20 campaign.
David Luiz's future has also been questioned, but it now seems likely that the Brazilian will extend his stay, and he could be joined at the heart of the defence by William Saliba, who has spent this season on loan with Saint-Etienne after agreeing to join Arsenal last summer.
Nicolas Pepe and Mesut Ozil will both feel that they should be starting for the club during the 2020-21 campaign; a potential replacement for Ozil has been discussed, but it seems unlikely that a big-money deal will happen this summer due to the financial impact of the coronavirus pandemic.
There is certainly a chance that the club could move for a new striker if Aubameyang leaves but whether they can get a deal over the line in the current market is questionable.