The aim of this study was to isolate, identify and quantify soluble free phenolics, conjugated acid-hydrolysable phenolics (AHP) and alkaline-hydrolysable phenolics, and bound phenolics (BP) fractions from two tomato varieties (saladette and grape) and an industrial tomato by-product, as well as, to determine their antioxidant capacity. Phenolic composition was determined using Folin–Ciocalteu’s method and HPLC–DAD. AHP were predominant in grape and saladette tomato extracts (91.47 ± 17.28 mg gallic acid equivalents (GAE) per g dry extract (DE) and 57.41 ± 8.80 mg GAE per g DE, respectively), while BP form was predominant in tomato by-product (51.30 ± 10.91 GAE per g DE). AHP extract of grape tomato presented the highest antioxidant capacity by DPPH assay (252.35 ± 42.55 μmol trolox equiv (TE) per g DE). In the case of ORAC assay, AHP fractions from both grape (1005.19 ± 138.52 μmol TE per g DE) and saladette tomatoes (804.16 ± 131.45 μmol TE per g DE), and BP fraction from by-product (852.40 ± 71.46 μmol TE per g DE) showed the highest ORAC values. Caffeic acid was the most abundant phenolic acid and it was found mainly in its conjugated forms. Naringenin was the most abundant flavonoid and it was mainly detected in bound form. Our analysis allowed a better characterization of phenolic compounds in whole tomato and by-product, remarking the importance of the fractionation. The valorization of the industrial tomato by-product, through the use of its different fractions of phenolic antioxidant compounds, could generate additional income to the tomato industry and reduce the waste disposal problem.