The increasing demand for safe and durable feed materials highlights the need for processing methods that simultaneously enhance physical quality and reduce microbiological contamination. Extrusion technology offers a promising solution by combining thermal and mechanical effects that improve binding performance while inactivating fungal spores present in cereal grains. In this study, maize, barley, sorghum, soybean, and wheat grains naturally contaminated with fungal spores were subjected to extrusion prior to pelleting. The physical properties of the resulting pellets, including bulk density, physical density, and kinetic durability, were evaluated and compared with those obtained from ground (non-extruded) grains. Pellets containing extruded grains generally exhibited higher physical density, with the highest value recorded for pellets containing extruded mould-infected sorghum grain (1179.82 kg·m−3) and the lowest for pellets containing healthy soybeans (1063.63 kg·m−3). The kinetic durability of extruded cereal pellets increased on average by 4.02%, enhancing their resistance to mechanical stress during transport and storage. Microbiological analyses confirmed a significant reduction in fungal colony-forming units (CFUs) after extrusion and pelleting, ranging from 27% to 65%, depending on the cereal type. The most pronounced reduction was observed in maize-based pellets contaminated with mould spores, decreasing from 1.70 × 105 to 6.03 × 104 CFU·g−1. These results demonstrate that extrusion is an effective method for producing cereal-based feed materials with improved physical quality and enhanced microbiological safety, contributing to more sustainable feed production.