Kick-off was delayed by an hour on Thursday night, as swathes of extra riot police were deployed in a bid to contain rowdy fans at the north London grounds.
Swarms of German fans attended the match after marching through the streets of central London earlier in the day.
The Met announced they were dealing with "disorder" at the game and said it would be delayed in the interests of crowd safety.
When the match kicked off at 9.05pm, emerged of fans letting off flares in the crowds and some wearing FC Koln scarves seated in the home section.
And videos showed some barging through barriers as mounted police attempted to contain them.
Both clubs had been in dialogue with UEFA over a possible postponement before a decision to go ahead was confirmed a little over 30 minutes before kick-off.
Another video appeared to show Cologne fans singing loudly in Arsenal's home section of the stadium.
In Pictures | Arsenal vs Cologne | 14/09/17
As a helicopter hovered overhead, police formed a line in a bid to hold back the crowds of fans.
A statement from the Metropolitan Police read: "Officers are dealing with disorder at the Emirates Stadium where fans have gathered for the Arsenal vs FC Koln match.
"A policing plan is in place for the game. Additional officers have been deployed."
They later announced that four people had been arrested on suspicion of public order offences.
Arsenal added: “The players were relaxed and preparing for the game despite the delay. The decision to go ahead was the best option and the safest option."
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Though only 3,000 tickets were allocated to travelling Cologne fans, an estimated 20,000 turned up for their club’s first European tie in 25 years.
The large mass of travelling supporters outside the away entrance were blocking many home supporters from taking their seats.
Confirmation of the delay came through at just after 7pm, at which time little over a hundred supporters had been able to make their way into the Emirates Stadium.
The match chaos came hours after fighting had broken out on Oxford Street involving German visitors.
The supporters of German side FC Köln descended on Oxford Street and parts of the West End - marching through the streets carrying flares and chanting.
An Arsenal spokesperson said that the delay had not been due to any concerns over further violence but for health and safety reasons with regards to home fans making their way into the ground.