Experiments with elderberry genotypes, ripening stage and pectinolysis were carried out in order to investigate the possibility to improve different quality characteristics of elderberry juice. Raw juice was processed using either an optimised method with respect to enzyme concentration and treatment time or produced directly without any enzymatic treatment. Neochlorogenic acid, chlorogenic acid, cyanidin-3-sambubioside-5-glucoside, cyanidin-3,5-diglucoside, cyanidin-3-sambubioside, cyanidin-3-glucoside, quercetin-3-rutinoside (rutin) and quercetin-3-glucoside (isoquercitrin) were identified in the raw juice by liquid chromatography-mass spectrometry (LC-MS) and quantified by high-performance liquid chromatography-diode array detection (HPLC-DAD). The content of phenolic acids and flavonoids in elderberries were shown to be affected by berry development stage at harvest (ripening stage). Furthermore, a considerable variation in juice yield and physicochemical properties such as turbidity, soluble solids, titratable acidity, and content of phenolic acids and flavonoids was found between juices processed from elderberries by pectinolysis of different elderberry genotypes. Pectinolysis appeared not to have any major effect on juice yield and the content of phenolic acids and flavonoids in the juice compared to non-enzymatic processed juice. Factor analysis revealed correlations among quality characteristics such as soluble solids, titratable acidity, turbidity, and content of phenolic acids and flavonoids and it is shown that these correlations may be useful for the selection of elderberry genotypes best suited for the preparation of juice.