The use of a blend of chickpea and pumpkin seed press cake flours in the production of gluten-free crackers represents a promising strategy to address nutritional gaps and meet the growing demand for healthier gluten-free options. To test this assumption, an in vitro digestion method was employed to assess changes in total phenolic content, antioxidant activity, protein composition, electrophoretic patterns, and mineral content of gluten-free crackers formulated using these raw materials before and after digestion. The crackers were produced substituting 20% and 35% of chickpea flour by using two types of pumpkin seed press cake flour, one from virgin oil pressing (VFC) and the other from cold-pressed oil pressing (CFC). This approach aimed to assess how the treatment history of the pumpkin seed press cake flour affected the tested parameters. All samples displayed a 3- to 4-fold increase in total phenolic content after in vitro digestion. A noticeable enhancement in antioxidant activity is observed, where CFC samples showed higher values compared to VFC samples. The control sample and 35CFC sample present similar protein digestibility values (%), 76.97 and 77.05 respectively, while other crackers showed significantly lower digestibility. Incorporation of pumpkin seed press cake flours leads to a substantial increase in mineral content, notably zinc (up to 2-fold), iron (up to 40%), and magnesium (up to 2.5 fold). Overall, the study provides valuable insights into the utilization of pumpkin seed press cake as a potential source of bioactive compounds, emphasizing its significance beyond its traditional role as a by-product.