Pears (Pyrus communis L.) and apples (Malus domestica Borkh.) are two of the most popular fruits worldwide. The phenolic compounds they offer are associated with human health benefits due to their antioxidant properties. Since these fruits’ by-products are not yet fully exploited, it is important to characterize them, especially in terms of their antioxidant properties. The aim of this study was to determine the antioxidant properties of old traditional cultivars, six regional pear cultivars and five regional apple cultivars grown in the Alcobaça region (Portugal). Antioxidant capacity assays were used to evaluate the antioxidant properties. Generally, the antioxidant capacity, total phenolics content (TPC), and total flavonoids content (TFC) of fruit byproducts (both seeds and peels) were higher than the corresponding mesocarp, indicating their potential as sources of beneficial antioxidant compounds. Moreover, a UHPLC-ToF-MS method was optimized and validated in order to quantify 21 distinct phenolics in these fruit samples. The analytical method’s suitability for quantifying phenolic compounds was demonstrated by an evaluation of linearity, limit of detection, limit of quantification, precision and accuracy. This method was used to determine the phenolic composition of samples of regional (local) cultivars. The phenolics in the fruit samples with the highest concentrations were phlorizin and chlorogenic acid. Principal component analysis (PCA) was used to separate distinct fruit species while emphasizing their similarities and differences.