By-products generated in the agri-food industry are frequently regarded as waste, despite their significant potential for reutilization as valuable raw materials with both nutritional and functional properties. Nigella and flaxseed pomace, as rich sources of bioactive compounds, have the capacity to enhance the nutritional profile and functional characteristics of extruded products while simultaneously contributing to the reduction in food waste. Uniquely, the present study analyzed the effect of extrusion-cooking process conditions on the efficiency, energy consumption, and selected physical properties of extrudates enriched with nigella and flaxseed pomace. The samples were made using a single-screw extruder-cooker. Two plasticizing (L/D 16 and 20) systems were compared. The highest efficiency, 23.16 kg/h, was reached using 20% nigella pomace with the L/D 16 system. During the whole process, the specific mechanical energy ranged from 0.006 to 0.105 kWh/kg. New information was obtained on the interaction between pomace content and the physical properties of the extrudates. The results showed that the use of 10% nigella pomace maximized the WAI 4.90 and WSI 11.73% for pellets with 30% of nigella seed pomace in the L/D 20 and influenced the change in bulk density, indicating a double innovation: an improvement in extrudate quality and the efficient use of by-products.