Purees and concentrates are intermediate products in the elaboration of commercial fruit juices. In this paper, the phenolic composition was established and quantified in a large number of samples of peach and apple purees and concentrates. Different benzoic acids and aldehydes, cinnamic acids and their derivatives, flavan-3-ols, procyanidins, flavonols, and dihydrochalcones have been identified. The concentration of cinnamic acids and derivatives is higher in the concentrates than in the purees for both fruits. However, flavan-3-ols and procyanidins are only present in the purees. Peach-based products are completely devoid of flavonol and dihydrochalcone derivatives due to the removal of the skin of the fruit in the manufacturing process. On the other hand, different quercetin and phoretin glycosides were detected in apple purees and concentrates. The results show that phenolic compounds can prove to be helpful in the characterization of fruit purees and concentrates as well as in the detection of adulterations in the manufacturing of commercial fruit juices from these intermediates.