In recent years, food industries have produced a large volume of waste, which is an ecological and economic problem. Fruit and vegetable by-products can also be promising sources of functional compounds, with documented pro-health potential. The goal of the study was to evaluate the impact of the addition of various concentrations of onion skin powder on the antioxidant and anti-inflammatory properties associated with changes in the quercetin content in uncooked and cooked pastas. The total contents of phenolic acids, quercetin, and antioxidant activity were determined. The anti-inflammatory activity was demonstrated by inhibitory effects on lipoxygenase (LOX) in vitro activity. Dry onion skin is the source of quercetin in analyzed pastas. The concentrations of these compounds gradually and significantly increased with increases in the vegetable component in fortified pastas. Additionally, a positive correlation between the content of phenolic compounds and antioxidant activity of pastas fortified with onion skin powder was noted. The process of cooking caused enhancement in the antioxidant and anti-inflammatory potential. These qualities of pastas resulted from the presence of dry onion skin with high pro-health activities. Fortification of pasta with onion skin powder could be a starting point to benefit onion industrial by-products and produce new healthy food products.