The amino acid tryptophan and its derived molecules serotonin and melatonin are involved in a wide range of physiological functions that contribute significantly to human health, namely antioxidant, immune-active, and neurological properties. Grapes and wine are a source of these compounds, but their presence in wine by-products remains underexplored. Therefore, the aim of this work was the identification and quantification of tryptophan, serotonin, and melatonin in winery by-products (grape stems, grape pomace, and wine lees) by ultra-high performance liquid chromatography coupled to electrospray ionization and mass spectrometer with triple-quadrupole technology (UHPLC-ESI-QqQ-MS/MS), as well as the evaluation of the extracts obtained (by applying specific extraction conditions for each of them) for their antioxidant and reducing capacity (by three different and complementary methods: FRAP, ABTS•+, and ORAC). Furthermore, correlation analyses were developed to establish the contribution of the different analytes to the total antioxidant activity. The main results obtained pointed out grape stems as the by-product with the highest tryptophan content (96.28 mg/kg dw) and antioxidant capacity (142.86, 166.72, and 363.24 mmol TE/kg dw, FRAP, ABTS•+, and ORAC, respectively), while serotonin and melatonin were the predominant derivatives in grape pomace (0.086 and 0.902 µg/kg dw, respectively). The antioxidant capacity of the standards was also analysed at the concentrations found in the matrices studied. A significant correlation was found between the concentration of the pure tryptophan standard and the antioxidant capacity (ABTS•+, r2 = 0.891 at p < 0.001 (***); FRAP, r2 = 0.885 at p < 0.01 (**); and ORAC, r2 = 0.854 at p < 0.01 (**)). According to these results, winery by-products can be highlighted as valuable materials to be used as novel ingredients containing tryptophan, serotonin, and melatonin, while tryptophan was identified as the most relevant contributor (out of phenolic compounds) to the antioxidant capacity exhibited by wine by-products.