And Pierre-Emerick Aubameyang doubled the lead after finding himself free in the box, but Everton fans will be disgruntled after replays showed the Gabonese striker way offside.
Emery, pictured, has also inherited the former manager's weird approach to the transfer window too, with seemingly astute signings in goalkeeper Bernd Leno and defensive midfielder Lucas Torreira benched or unused in favour of the ageing and rather faulty Petr Cech and 19-year-old French midfielder Matteo Guendouzi.
It was the latest in a long line of defensive disappointments for Arsenal, who have failed to keep a clean-sheet in any of Emery's six matches in charge.
But the Spaniard doesn't believe that should be used as an excuse for Arsenal's fragile defending. "I think we need to improve this". "It's clear we have a very competitive team and I'm confident in them".
Leno, a close-season signing from Bayer Leverkusen, could be key to Emery's defensive rebuild. When the Switzerland worldwide had his latest brain fade - putting Everton on the counter-attack by gifting them the ball from a free-kick - it was his midfield partner who swept up to salvage the situation.
Former Arsenal man Theo Walcott was also guilty of squandering a good chance for the visitors, failing to get enough on his attempted chip over Cech when racing in behind, and Everton were so almost punished in the closing stages of the first half. I will work hard every day to play more games.
"It is a little bit more risky to play because we don't want to kick the ball up front", he added.
Back in January, the 29-year-old opted to take on a new challenge as Everton made a £20 million ($26m) move for his services.
Everton, on the other hand, have made three changes to the side that was beaten by West Ham United last weekend.
"It's something we analysed during the week".
In midfield, Tom Davies came in for Morgan Schneiderlin and was handed the captain's armband, while in attack, Dominic Calvert-Lewin moved into the centre-forward role instead of Cenk Tosun and Richarlison returned in the wide left role.