The Latics have received a fee of around £600,000 for Granqvist, who joined them on loan from Helsingborgs in January 2007 before completing a permanent move last summer.
"I see Groningen as a club where I can develop myself," said the 23 year old after signing a four-year contract.
"I haven't played a lot at Wigan Athletic and it was very important for me to choose a club which plays the football I like to play.
"I am a player who likes to start attacks from the defence and not only use the long ball. I am still young and want to become better."