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. In the context of global climate change the extensive diversity of compounds and variation of biosynthesis within species may play a key role to mitigate the increased frequency of stressful events such as drought, heat waves or emergent pathogens. Here, we study the genetic basis of leaf SMs natural variation in nine European provenances of sessile oaks and investigate signature of selections along the genome. 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 leaf specialized metabolites. In addition, we used whole genome low-depth sequencing to genotype all individuals for 1.4M genetic markers. We then performed genome-wide association analyses, identified candidate genes underlying the variation of leaf SMs and compared signatures of selection at these genes to the rest of the genome. 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 of most leaf SMs is unlikely to be locally adaptive, and that varying selective pressures may act locally to maintain diversity at loci associated with leaf SM variation.