Kuenen studied at the University of Groningen, where he received both his Doctorandus degree and in 1972 his Doctorate (PhD) under the supervision of Professor Dr. Hans Veldkamp.
After a short post-doc at the University of California in Los Angeles (USA), he returned as a senior lecturer to Groningen.
Kuenen's initial research interests were (the application of) bacteria involved in the natural sulfur cycle and yeast physiology and metabolism.
In addition, his research has been focussed on (halo) alkaliphilic sulfur-oxidizing bacteria from soda lakes.
In 2004 Gijs Kuenen became a Knight in the Order of the Netherlands Lion, In 2005 he was elected Fellow of the American Academy of Microbiology.