Arsenal were desperate to offload Mustafi and Emery even publicly told the German he had to leave as he would not play if he remained at the Emirates.
Emery revealed that after telling Mustafi he was surplus to requirements, he had another chat with the 27-year-old.
‘Mustafi decided to be here and when he decided to be here, he’s like any other player,’ said Emery.
‘Of course I respect his decision. When he decided I spoke to him and said, “You’re one more in the squad, I’m going to work with you as other players”.
‘I don’t know exactly who was in his decision [to stay], but when he decided to stay here, it’s another player in the squad.’
Mustafi reportedly had offers from Italy, but the window closed without a move materilising.
The centre-back is yet to make a matchday squad this season and is likely to be overlooked again this weekend when Arsenal resume club action.
Arsenal travel to Watford on Sunday and Mustafi is currently behind Calum Chambers, Sokratis and David Luiz in the centre-back pecking order.
While Mustafi decided to remain at Arsenal, the Gunners did sell several high-profile stars, including Mohamed Elneny, Laurent Koscielny, Nacho Monreal and Alex Iwobi, with Danny Welbeck and Aaron Ramsey leaving at the end of their contracts.