Waste streams from cereal-based food production processes, rich in organic matter and carbohydrates, have untapped potential for biogas production. This study uniquely investigated the extrusion-cooking process conditions, physical properties and biogas efficiency of snack pellets enriched with plant pomace (apple, chokeberry, pumpkin, flaxseed and nigella seeds) at different levels (10, 20 and 30%), produced using a single-screw extruder-cooker. The highest efficiency obtained in the extrusion-cooking process (18.20 kg/h) was observed for pellets with the addition of 30% flaxseed pomace. The SME value during the entire process was in the range of 0.015–0.072 kWh/kg. New insights into the interaction between the inclusion of pomace, the physical properties of the extrudate and the anaerobic fermentation efficiency were obtained. The results show that 30% chokeberry extrudate maximized methane production (51.39% gas), demonstrating a double innovation: improving snack pellet quality and converting food waste into renewable energy.