Wild albino and blue bilberry fruit were analyzed to compare different fruit characteristics linked to the composition of primary and secondary metabolites. Compounds were identified using HPLC–MS and standard quality parameters were determined. Albino berries were significantly smaller, accumulated less water and were characterized by 23% higher dry weight. Soluble solids content and pH value were higher in albino bilberry and their surface was lighter and characterized by a yellow hue. Both bilberry forms accumulated identical individual sugars and organic acids; however, the albino form had 33% higher content of total sugars and 9% higher content of total organic acids compared to the blue type. Fifteen anthocyanins were identified in both forms, but in albino bilberries, individual anthocyanins were only detected in traces. Blue bilberry contained 1.6-fold higher levels of flavanols, 2.1-fold higher levels of flavonols, 2.5-fold higher levels of hydroxycinnamic acid derivatives and consequently, 4.6-fold higher total phenolic content.