The duo have been linked with a move away in the summer, with Mustafi currently negotiating with Italian side, AS Roma over a loan deal, while Elneny is understood to be a target for Galatasary.
Emery has revealed that they are not in his plans as he looks to take the club back to the UEFA Champions League next season.
Unai Emery is making it very clear, both privately and publicly, that Shkodran Mustafi & Mohamed Elneny have no future at #AFC.— Sam Dean (@SamJDean) August 22, 2019
“They know the situation. I think it’s positive for them to leave and to sign for another team where they can be protagonists, they can be happy.”
"Elneny and Mustafi know their position in the squad and really I want the players to be happy here, I want the players to be protagonists here. Last year with Mustafi and Mo, when they didn’t play they weren’t happy and I spoke with them a lot of times last year and this pre-season and I think it is positive for them to leave and sign for another team where they can be protagonists and be happy and continue their careers," Emery said as quoted by Dailymail.
"They are very big players but for one circumstance or another, they are going to have less chances to show their capacity or to be happy with us and the minutes they play in matches.
But they know the situation and really, really I am wishing the best for them and I think now the best for them is to be protagonists in another team and sign and to get another challenge for them with another team," he added.
The German who is yet to play a single minute for the club this season, has so made 112 appearances while Elneny has been with the Gunners for over four seasons making 89 appearances.