Van Groeningen was born in Ghent. His parents were hippies who led a very liberal lifestyle. He has an older brother, Seppe. After his parents’ divorce, they lived in the same house, but each with a new partner. His father started a live music club ‘The Charlatan’ when he was twelve-years-old, which became the inspiration for his film Belgica. He studied at the Royal Academy of Fine Arts (KASK) and graduated in 2000 with a Masters of Audiovisual Arts, his masters thesis was the short film 50CC. He and Belgian actress Charlotte Vandermeersch have a son, Rufus, who was born in 2018. He is fluent in several languages, including Flemish Dutch, French, and English.

His fifth feature film, Belgica (2016), follows the lives of two brothers who start a nightclub but quickly gets swept up in hedonistic pursuits. The film was based upon two real-life brothers who bought ‘The Charlatan’, a music club owned by his father, in 2000 and managed it for seven years. The film premiered at Sundance Film Festival where he won the Best Director prize in the World Cinema Dramatic section. The film received mixed reviews from critics but was praised for the soundtrack created by the Flemish band Soulwax, who had previously collaborated with Van Groeningen on Steve + Sky.

His fourth feature film, The Broken Circle Breakdown (2012), starred Johan Heldenbergh and Veerle Baetens as Didier and Elise, a bohemian couple that loses their daughter to cancer. It is an adaptation of a stage play originally written and directed by Heldenbergh. The film was a critical and commercial success, and became the most watched Flemish film in Belgium of the year. The film was selected as the Belgian entry for Best Foreign Language Film at the 86th Academy Awards, and was on the nominated shortlist. He was invited to become a member of Academy of Motion Picture Arts and Sciences in 2014.

After graduating from college, van Groeningen directed several short films, and written and directed several stage plays. He embarked on a long-term collaboration with Dirk Impens, originally his professor at KASK, who produced all five of Van Groeningen’s feature films from 2004 to 2016 under his production company Menuet. Impens announced he was closing down Menuet in July 2017.