Around 20,000 German supporters are thought to have descended on the capital yesterday for the encounter, despite the club's official away allocation standing at just 2,900.
Kickoff in the match was delayed to 9.05pm as ticketless fans stormed the stadium attempting to gain access, while many more fans posed as Gunners supporters in order to be admitted.
As a result, many Arsenal fans reported being surrounded by Koln counterparts in the home areas of the Emirates, and ITV's political editor Robert Peston - a season-ticketed Gunners supporter - took to Twitter to condemn their 'disgraceful' behaviour.
Chaos at Arsenal pic.twitter.com/iDOIh82vtv— Robert Peston (@Peston) September 14, 2017
He wrote: "These Cologne fans are a disgrace. Nazi salutes. Peeing in doorsteps. My European solidarity being tested"
Arsenal went on to win the encounter 3-1 to take an early lead in their Europa League group.