The present research presents a comprehensive characterization of polyphenols from peach, pear, and plum using liquid chromatography coupled with electrospray ionization quadrupole-time-of-flight-mass spectrometry (LC-ESI-QTOF-MS/MS), followed by the determination of their antioxidant potential. Plums showed the highest total phenolic content (TPC; 0.62 mg GAE/g), while peaches showed the highest total flavonoid content (TFC; 0.29 mg QE/g), also corresponding to their high scavenging activities (i.e., DPPH, ABTS, FRAP, and TAC). In all three fruit samples, a total of 51 polyphenolic compounds were tentatively identified and were mainly characterized from hydroxybenzoic acids, hydroxycinnamic acids, hydroxyphenylpentanoic acids, flavanols, flavonols, and isoflavonoids subclasses. Twenty targeted phenolic compounds were quantified using high-performance liquid chromatography with photodiode array detection (HPLC-PDA). The plum cultivar showed the highest content of phenolic acids (chlorogenic acid, 11.86 mg/100 g), whereas peach samples showed the highest concentration of flavonoids (catechin, 7.31 mg/100 g), as compared to pear. Based on these findings, the present research contributes and complements the current characterization data of these fruits presented in the literature, as well as ensures and encourages the utilization of these fruits in different food, feed, and nutraceutical industries.