The match was delayed by an hour after 20,000 Cologne fans arrived at the Emirates and attempted to get into the ground.
When the game finally started, Arsenal bossed possession of the ball and were loudly jeered and whistled by the large Cologne support.
But that turned to rapturous cheers and applause in the ninth minute thanks to a stunning goal from Jhon Cordoba.
A ball was played over the Arsenal defence and David Ospina came off his line to clear but miscued his kick and when the ball found Cordoba, he struck a driven shot over the keeper from 40 yards out.
Arsenal attempted to respond but struggled to put anything clear cut together.
Several players were guilty of misplaced passes and when the half-time whistle went, the boos from the home crowd said it all.
But summer signing Sead Kolasinac came off the bench at the interval and made an immediate impact with a thumping finish.
Alexis Sanchez then got his first goal of the season with a stunning shot from outside the box.
And Hector Bellerin completed the scoring in the 81st minute when he poked home after Theo Walcott’s shot was saved.