Sergio Aguero scored his 10th Premier League hat-trick to condemn the Gunners to a 3-1 defeat , which keeps them sixth in the table.
Emery has inherited this dismal run from Arsene Wenger but believes the problems are not physiological.
"The mentality is the same," said the Spaniard, whose side have recorded home wins over Chelsea and Spurs this term. "When players are better they feel that.
“Our players have the mentality. When we are worse than the opposition we feel that. There are good things with some players. We have players with good possibilities.”
Not since the North Londoners beat City 2-0 in January 2015 have they overcome a club in the higher echelons of the top flight.
That run includes seven draws and 16 defeats, scoring just 24 goals and conceding 53.
Aguero opened the scoring after 51 seconds but Laurent Koscielny levelled to stem the flow.
But there still remained an inevitability about the result and Aguero put the defending champions back in-front before completing his treble after the hour mark .
He added: "They showed their superiority today. Two different times in the first half we struggled but together, defensively, being strong in some moments and keeping the result like we can have an option.
“All the small details we need to work well and not concede [weren’t there]. The first half we can be with some optimism to do something different in the second half.
“It was different. We opened the match more than the first half. They showed today with the possession against us, getting our defence position very deep, they can win like in the first half. The result is the difference between us.”
Shkodran Mustafi was withdrawn with 11 minutes remaining and replaced by Konstantinos Mavropanos, who made his first appearance under Emery.
The boss revealed the German has been suffering with a facial problem and was substituted as a precaution.