The study focused on the distribution of polyphenolic compounds, iridoids, organic acids, and sugars, as well as in vitro antioxidant, anti-inflammatory, antidiabetic, antiproliferation, and antibacterial potential, and physicochemical properties between the skin and flesh of 10 haskap berry (Lonicera caerulea var. kamtschatica Sevast.) cultivars. It was found that the content of individual bioactive compounds significantly depended on the fruit cultivar and the analyzed morphological part. Anthocyanins, kaempferol derivatives and iridoids dominated in the skin, which significantly correlated with most of the analyzed health-promoting properties. In turn, the flesh showed a higher content of quercetin derivatives, sugars and organic acids. No differences were found in the content of phenolic acids, flavan-3-ols and antibacterial activity. The most beneficial properties were shown for the cultivar (cv.) ‘Honeybee’. The study suggests that haskap fruit skin is a valuable raw material for use in the pharmaceutical and food industries.