Specialized or secondary metabolites (SMs) play a key role in plant resistance against abiotic stresses and defences against bioaggressors. For example, in sessile oaks Quercus petraea , phenolics contribute to reduce herbivore damage and improve drought resistance. Here, we explored the natural variation of SMs in nine European provenances of sessile oaks and aimed to detect its underlying genetic bases. We sampled mature leaves from high and low branches on 225 sessile oak trees located in a common garden and used untargeted metabolomics to characterise the variation of 219 specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype individuals for 1.4M genetic markers. We then performed genome-wide association analyses to identify the genetic bases underlying the variation of leaf SMs. We found that leaf SMs displayed extensive within-provenance variation, but very little differentiation between provenances. For ∼10% of the metabolites we detected, most of this variation could be explained by a single genetic marker. Our results suggest that genetic variation for most leaf SMs is unlikely to be locally adaptive, and that selective pressures may act locally to maintain diversity at loci associated with leaf SM variation within oak populations.