In this study, our research aim was to assess the influence of pumpkin seed flour addition on the antioxidant properties, consumer acceptability, functional properties, and texture of wafers. The in vitro gastrointestinal digestion process was used to assess the effectiveness of fortification in terms of the potential bioavailability of phenolic compounds and peptides. The antioxidant activity of the obtained hydrolysates and potentially bioavailable fractions (≤3.5 kDa) was tested. The highest antiradical activity and Fe2+ chelation ability (IC50) were noted for the fraction obtained from wafers with the greatest addition of pumpkin seed flour—Pf4 (0.49 mg/mL for ABTS+*, 3.84 mg/mL for DPPH*, and 2.04 mg/mL for Fe2+ chelation). The addition of pumpkin seed flour caused the color of the wafers to change to a darker one (24.46% differences in L* between C and P4), which influenced consumer ratings. This study shows that adding pumpkin seed flour increases the peptide and phenolic contents of wafers (1.13 mg/mL and 1.01 mg/mL of peptides and 0.429 mg/mL and 0.351 mg/mL of phenolics for P4 and C hydrolysates, respectively) and enhances their antioxidant activity, with only minimal effects on taste, aroma, crispness, water and fat adsorption capacity, and foaming ability. Fractions ≤ 3.5 kDa showed greater antioxidative activity than hydrolysates, and the addition of pumpkin seed flour improved these properties. To sum up, pumpkin seeds are a valuable source of antioxidant compounds (phenolic compounds and peptides) and can be used to enrich various products.