Kick-off was pushed back by one hour to 21.05 BST due to crowd congestion in London, with a reported 20,000 away supporters said to have travelled from Germany.
Arsenal attempted to respond in the rest of the first-half but were unable to do so and will now be hoping that there first Europa League game will not end in tatters. They knew last season was bad but the fruits of that rotten season have now come to fruition.
Arsene Wenger has opted to make several changes from the side which beat Bournemouth comfortably at the weekend as the Chilean worldwide is afforded his first start at the Emirates Stadium this season.
He could have scored another two, but struck a free-kick straight at Horn and shanked wide from inside the area.
Season 2016/17 for Cologne with confidence can be called successful.
The Europa League final will be held at the Parc Olympique Lyonnais in May next year and Lacazette is eyeing a return to his home town with Arsenal to win the competition in front of his family and friends.
Irma kills Guyanese in British Virgin Islands
He'll be visiting the most hard-hit places of the island before heading to the British Virgin Islands . Nine tonnes of food and water supplies are due to be flown out to Anguilla imminently, Sir Alan said .
"The majority will be a little more realistic though - the club are now bottom of the Bundesliga, so any decent European adventure would be good, I expect".
Videos emerged on social media of the German side's support briefly bringing parts of central London to a standstill as they threw bottles and let off flares while making their way to the ground.
More than a dozen police officers wearing helmets could be seen entering the ground at the east stand as the game kicked off.
Asked if the number of Cologne fans at the match was a surprise, Arsenal manager Arsene Wenger told reporters: "They were very clever". The Gunners face German side Cologne in their opening fixture on Thursday. Which means that they will not be featuring in the match.
But they qualified for the Europa League after finishing fifth last term.
It was not until after the break - and a switch to a 4-2-3-1 formation from three at the back - that the Gunners were able to display the dominance expected of them in their first season outside of the Champions League in 19 years.
Cologne stunned the Emirates crowd in the ninth minute when Cordoba struck from 30 yards following a poor clearance from Arsenal goalkeeper David Ospina who was well off his line.