Aronia, haskap, and goji berries are characterized by their high content of bioactive compounds and their beneficial health properties, as well as their resistance to harsh agronomic conditions. In this work, cultivars of these species growing in a mountainous region of central-western Spain were characterized by analyzing physicochemical parameters and bioactive compounds. Goji fruits showed the highest TSS content and the lowest acidity values. The sugar profile suggested that goji cultivars will have a higher sweetness due to higher fructose and glucose content. However, aronia cultivars will be the least sweet due to their high sorbitol content. The total organic acid content was much higher in aronia and haskap than in goji fruits, and the profile varied according to species. The total phenolic content was significantly higher in aronia fruits. A total of 15 phenolic compounds were detected with anthocyanins being predominant in aronia and haskap berries, however, they were not detected in goji fruits. Nevertheless, carotenoid compounds were found in goji berries, and non-detected in aronia and haskap fruits. Aronia fruits showed the highest antioxidant capacity compared to haskap and goji fruits. The PCA analysis allowed us to classify the samples and determine which parameters have the greatest influence.