The Spaniard, who spent time on loan at Tranmere Rovers last season, made three Premier League appearances towards the end of the campaign, and was named in the squad for the FA Cup final victory over Manchester City.
Golobart was out of contract, and following Wigan's relegation FC Koln director Jorg Jakobs confirmed the Bosman free transfer signing of the defender.
"We are pleased to announce the signature of Roman Golobart," Jakobs told the club's official website.
"We are happy that he has agreed to join our club despite having the chance to prolong his contract with Wigan Athletic, and the chance to continue playing in the top leagues of England.
"He has decided in favour of our club as he is keen to make good progress within our first-team squad."
The 21-year-old began his youth career at Espanyol, where his father Joan was a player in the 1980s.