Over the last few years, diploid strawberry (Fragaria vesca) has been recognized as a model species for applied research of cultivated strawberry (Fragaria × ananassa) that is one of the most economically important crops. Berries, particularly strawberries, are known for their high antioxidant capacity due to a high concentration of (poly) phenolic compounds. Studies have already characterized the phenolic composition of fruits from sets of cultivated strawberries but the quantification of phenolics in a Fragaria mapping population has not been reported, yet. The metabolite profiling of a F. vesca near isogenic line (NIL) collection by LC-MS allowed the unambiguous identification of 22 (poly)-phenols, including anthocyanins, flavonols, flavan-3-ols, flavanones, hydroxycinnamic acid derivatives, and ellagic acid in the diploid strawberry fruit. The variability in the collection revealed that the genetic factor was more decisive than the environmental factor for the accumulation of 18 of the 24 compounds. Genotyping the NIL collection with the Axiom IStraw90 SNPs array, we were able to map 76 stable QTLs controlling accumulation of the (poly)-phenolic compounds. They provide a powerful new tool to characterise candidate genes to increase the antioxidant capacity of fruits and produce healthier strawberries for consumers.