The man, a 28-year-old originally from Kosovo, was expelled from Germany and was supposed to be flown to Hungary.
He boarded the Lufthansa plane carrying 82 people from Munich to Budapest without a police escort.
But shortly after the plane took off he threatened the stewardess and the pilot decided to turn around and head back.
Police described the situation as “threatening”.
The plane was evacuated and one crew member sustained cuts on their hand.
Airport police said the man offered no resistance when he was arrested.