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<i>Lonicera caerulea</i> fruits are a rich source of vitamins, organic acids, and phenolic compounds, which are characterised by their health-promoting properties. The content of bioactive compounds in this fruit may vary depending on the cultivar and the harvest date. The fruits of the <i>L. caerulea</i> var. <i>kamtschatica</i> cultivars ‘Duet’ and ‘Aurora’ and the <i>L. caerulea</i> var. <i>emphyllocalyx</i> cultivars ‘Lori’, ‘Colin’ and ‘Willa’ were used in this study. <i>L. emphyllocalyx</i> fruit, especially the cultivar ‘Willa’, was characterised as having a higher acidity by an average of 29.96% compared to <i>L</i>. <i>kamtschatica</i>. The average ascorbic acid content of the <i>L</i>. <i>kamtschatica</i> fruit was 53.5 mg·100 g⁻¹ f.w., while <i>L. emphyllocalyx</i> fruit had an average content that was 14.14% lower. The antioxidant activity (determined by DPPH, FRAP, and ABTS) varied according to the cultivar and the species of fruit analysed. The total polyphenol content differed significantly depending on the cultivar analysed; fruits of the <i>L. emphyllocalyx</i> cultivar ‘Willa’ were characterised by the lowest content of total polyphenols—416.94 mg GAE·100 g⁻¹ f.w.—while the highest content of total polyphenols—747.85 GAE·100 g⁻¹ f.w.—was found in the fruits of the <i>L. emphyllocalyx</i> cultivar ‘Lori’. <i>Lonicera caerulea</i> fruits contained 26 different phenolic compounds in their compositions, of which the highest content was characterised by cyanidin 3-<i>O</i>-glucoside (average: 347.37 mg·100 g⁻¹). On the basis of this study, it appears that both <i>L</i>. <i>kamtschatica</i> fruits and <i>L. emphyllocalyx</i> fruits, especially of the cultivars ‘Lori’ and ‘Willa’, can be used in food processing.