The false fruits of apple (Malus domestica) and pear (Pyrus communis) are consumed all over the world, contributing to the dietary intake of health-promoting antioxidant phytochemicals. For example, polyphenols confer many beneficial effects (according to their chemical structure, bioavailability, and absorption efficiency in the gut) and the consumption of polyphenol-rich apple and pear fruits may therefore reduce the risk of some diseases. However, the content of such molecules is highly dependent on the specific fruit cultivar. To examine this metabolic diversity in detail, we used metabolomic analysis (NMR and HPLC-DAD/MS) to profile the metabolome of six apple and five pear cultivars. We also determined the antioxidant capacity of the extracts (FRAP assay) and correlated this with the metabolomic composition and abundance of specific metabolites. We observed the cultivar-specific accumulation of sugars, amino acids, malic acid, and various polyphenols, which was also related to the growing season for some cultivars. We found that the ancient Italian apple Pom Prussian was enriched for chlorogenic acid as well as more characteristic polyphenols (phloretin derivatives), the pear cultivar Abate Fetel was low in sucrose, and both cultivars displayed high in vitro antioxidant activity. These cultivars may, therefore, be particularly attractive to health-conscious consumers.