Eriobotrya japonica, commonly known as loquat, has been used traditionally for the treatment of different diseases. Herein, untargeted profiling based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was used to depict the phytochemical profile of loquat roots, leaves, stems, seeds, and fruits. This allowed the tentative annotation of 349 compounds, representing different phytochemical classes that included flavonoids, phenolic acids, lignans, stilbenes, and terpenoids. Among others, low molecular weight phenolics (tyrosol derivatives) and terpenoids were the most abundant phytochemicals. After that, in vitro antioxidant and enzyme inhibition assays were applied to investigate the biological activity of the different organs of Eriobotrya japonica. Roots of E. japonica exhibited the highest antioxidant capacity, showing 181.88, 275.48, 325.18, 169.74 mg Trolox equivalent (TE)/g in DPPH, ABTS, CUPRAC, and FRAP assays, respectively. Furthermore, the root extract of E. japonica strongly inhibited butyryl cholinesterase (3.64 mg galantamine equivalent (GALAE)/g), whereas leaves, stems, seeds, and fruits showed comparable inhibition of both acetyl and butyryl cholinesterases. All the investigated organs of E. japonica exhibited in vitro tyrosinase inhibition (57.27–71.61 mg Kojic Acid Equivalent (KAE)/g). Our findings suggest a potential food and pharmaceutical exploitation of different organs of E. japonica (mainly roots) in terms of enrichment with health-promoting phenolics and triterpenes.