Black fruits, especially blackberries and black currants, are highly appreciated by consumers due to their nutraceutical properties, which have reported health benefits. This study aimed to assess the fruit quality of the blackberry (cv. ‘Čačanska Bestrna’) and black currant (cv. ‘Čačanska Crna’) created at the Fruit Research Institute, Čačak (Republic of Serbia) by evaluating basic quality parameters (fruit weight, soluble solids), and content of primary (sugars and organic acids) and secondary (phenolic compounds) metabolites. Additionally, the study examined the quality of frozen and long-term frozen storage (6, 9, and 12 months). The results showed that ‘Čačanska Crna’ contained a high level of total soluble solids (15.23°Bx), sugars (93.06 mg g−1), and a high index of sweetness (159.48) as well as a high content of acids (34.35 mg g−1) in the fruit. Both species were found to contain forty-seven phenolic compounds, including phenolic acids, flavanols, and anthocyanins, analyzed using high performance liquid chromatography-mass spectrometry (HPLC-MS). ‘Čačanska Bestrna’ had the highest amounts of phenolic acids (66.85 mg 100 g−1) and flavanols (53.99 mg 100 g−1), whereas ‘Čačanska Crna’ showed the highest levels of flavonols (8.57 mg 100 g−1) and anthocyanins (139.11 mg 100 g−1). Furthermore, the study revealed that anthocyanins were the most abundant phenolic group in both blackberries and black currants, and their levels remained constant during frozen storage. The sugar content in both species remained unchanged, while the acid concentration increased over time in blackberries but remained consistent in black currants. Overall, the findings highlight the superior phenolic content, particularly anthocyanins, of the cultivars with black fruits selected in Serbia. These cultivars have great commercial potential for the fresh market and processing. Moreover, the study suggests that frozen storage is an effective method for preserving their quality and beneficial properties.