European football's governing body UEFA has charged Arsenal and FC Köln with a number of offences following last night's match in London.
The German club is facing four charges related to crowd disturbances, the setting off of fireworks, the throwing of objects and acts of vandalism.
Arsenal are facing sanction over blocked stairways in the away supporters section.
"Disciplinary proceedings have been opened following the UEFA Europa League group stage match between Arsenal and Cologne," a UEFA spokesperson said in a statement.
Thousands of FC Köln fans brought parts of London to a standstill last night.
The Guardian reports that an estimated 20,000 fans attempted to attend the match, despite an official allocation of only 3,000 tickets.
The UEFA Europa League fixture was the German side's return to European football after a 25 year hiatus.
The match was delayed by an hour in the interests of "fan safety" as massive crowds of Cologne supporters gathered around the stadium.
Vast numbers of away fans gained entrance to areas of the stadium designated for home supporters - prompting Arsenal to open a "full review" into how they acquired the tickets.
The club said it was 'very disappointing' that many tickets appeared to have been sold through touts.
Koln fans fighting with stewards inside Emirates stadium. Group arrived in home end and fought their way into away section. pic.twitter.com/7RC17WZyz2
— Richard Conway (@richard_conway) September 14, 2017
Fans with tickets are said to have had difficulty accessing the stadium in the first place amid huge crowds on the streets outside.
— Jack Marczewski (@j_cheski) September 14, 2017
Met Police say they responded to "reports of disorder" at the stadium, leading to the deployment of extra officers.
There were no reports of 'significant incidents', but five people were arrested on suspicion of public order offences.
Speaking about the delay, Arsenal coach Arsene Wenger said: "I thought they would not play the game, because I can’t see the police taking any risk. We live in a society of 100 per cent security and I thought they would never take a gamble to play this game when I saw the images around the stadium.
"But I must say our supporters as well dealt well with the situation as well and there was no aggravation."
On the subject of Cologne fans, he added: "They were very clever. I don’t know how they managed to infiltrate our fans and get everywhere but they did that very well."
The case against both clubs will be heard by UEFA's Control, Ethics and Disciplinary body on September 21st.