And it was Guendouzi who received the blame from his Arsenal teammates after Sterling bagged the first goal.
But Emery has insisted that he will not be parting ways with the 27-year-old any time soon.
The Gunners were threatening to come back into the match with City leading by Raheem Sterling's early goal, but Bernardo's top-corner effort was as perfectly timed off his laces as it was on the clock. Emery has commented recently that he wants his team to play like City, and he will demand intensity and pressing that was often lacking from his predecessor's teams.
City look as hungry as ever despite their record-breaking success last season, when they won the title with a record 100 points and also lifted the League Cup. He laid the ball back to Cech as Arsenal began another slow move forward, but the former Chelsea man's intended pass to Hector Bellerin was miscued and the ball trickled just wide of his own post and out for a corner.
Granit Xhaka, Shkodran Mustafi and Mesut Ozil all showed familiar flaws, and they were not the only ones to struggle.
"But he knows and his agent knows we like him and want him a lot". "Emery is going to need two or three transfer windows to sort out the personnel", added Gary Neville. Arsenal must watch long balls over the top, however - Aguero has punished them in that manner in the past, particularly in this year's Carabao Cup final.
It doesn't get much easier for Arsenal as they travel to Stamford Bridge next Saturday, while City play host to Huddersfield the following day.
But in the end it was not to be and Emery was honest in his analysis of the game.
Here is how you can catch all the action of this first big Premier League match of the season.
Emery will cling to those positives, but he will not be under any illusions about the challenge he faces to transform this Arsenal team.
"He trained just one week but we needed him today, and he did so well except when he was very exhausted at the end". The next chapter is underway, but Emery's work is only just beginning.