Here we authenticated single-varietal peach purees and pear juices on the basis of primary metabolite and phenolic compound analysis by Proton Nuclear Magnetic Resonance (1H-NMR) and Ultra Performance Liquid Chromatography coupled to Photodiode Array and Tandem Mass Spectrometry (UPLC-PDA-MS/MS), respectively. After suitable preprocessing, the 1H-NMR and chromatographic data were evaluated by principal component analysis (PCA). The PCA combining data from primary metabolites and phenolic compounds allowed the separation of the clusters in all cases, allowing discrimination of processed and unprocessed peach purees, both separately and pooled. The PCA of primary metabolites allowed the cluster separation of purees of distinct peach varieties but not between processed and non-processed purees. The PCA of phenolic compounds allowed better cluster separation than of primary metabolites. For pear juices, both PCA approaches allowed satisfactory discrimination of Alejandrina, Conference, and Blanquilla cultivars. These approaches may help to better control cultivar authenticity in fruit products. It could therefore contribute to the development of a process to achieve products characterized by a quality characteristic of a given cultivar.