Cornelian cherry (Cornus mas L.) belongs to a group of fruit and nut species growing in Europe considered to be underused economically, although it has been recognized as a potential regional “superfood” and as a source of valuable bioactive compounds. Phenotyping fruits of 30 accessions of an Austrian wildtype population of C. mas allowed to evaluate their nutraceutical potential. Ten fruits per accession were characterized by morphological and morphometric approaches. Biochemical analyses were performed to determine the respective amounts of vitamin C, sugars, anthocyanins, iridoids and flavonoids. Both datasets were subjected to statistical analyses. Morphological and morphometric characterization and biochemical analyses enabled the identification of the individuals with the highest economic value. Statistical treatment of data identified the most significant principal components. The first phenotypic profiling of bioactive compounds of wildtype C. mas in Austria yielded a high variability. Dealing with wildtype plants, this is not surprising. However, our results allow to select among the Austrian C. mas accessions the most interesting individuals for further breeding of this alternative fruit with interesting nutritional values.