Police had raised the alarm at around 12.15pm after a person managed to get into the secure area without passing through security checks.
A federal police spokeswoman told The Local that a 62-year-old Spanish man had managed to get in through an exit door "while trying to get to his aircraft as quickly as possible."
"He just picked the wrong route," she said.
Around 2,500 passengers were affected by the chaos at the terminal after the alarm was raised, airport spokespeople said in a press statement.
Things are getting back to normal at Terminal One although some flights are still delayed, the statement continued.
While five aircraft were prevented from taking off while police searched for the man, they all suffered only delays rather than cancellations.
Before the arrest bomb dogs were sent through the terminal to hunt for explosives and all passengers' identities were checked again.
Air traffic at Terminal Two went on as normal during the alert.
Security at Cologne-Bonn airport has regularly appeared in the headlines in recent months.
In March an undercover cop pushed her way through security to the air side without submitting herself to checks, setting off alarms.
And in April security inspectors reported that they had been able to smuggle weapons and bomb parts through the X-ray scanners at the airport undetected.