The aim of the present article was an in-depth characterization of cyanidine-rich red cabbage extracts and the identification of challenges emerging during the purification of their pigments. Two extraction procedures using either hot acidified or temperate water at its genuine pH were compared. LC-MS analyses revealed 20 mostly acylated anthocyanins, five aliphatic glucosinolates, and four indolic glucosinolates as non-volatile constituents. In addition, volatiles were characterized by HS-SPME-GC-MS. Whereas the glycosidic precursors do not impair the sensory properties, their enzymatic degradation products may evoke unpleasant flavors. The crude pigment extract obtained with hot acidified water contained low concentrations of C6 aldehydes, isothiocyanates, nitriles, and sulfides, and was selected for purification experiments. Amberlite XAD 16 HP, polyamide, chitosan, and lignosulfonate were used as adsorbents and flocculants. Particularly, Amberlite and lignosulfonate treatment diminished the content of glucosinolates and volatiles. Interestingly, indolic glucosinolates and acylated anthocyanins showed similar behavior in all purification procedures performed.