<p>A pilot-scale column reactor, with both anaerobic and aerobic zones, was used to examine the impact of localized anaerobic spots that naturally develop due to non-uniform aeration during the aerobic co-composting of SRM and manure. Specified Risk Materials (SRM)—a category of high-risk animal byproducts, including the brain, spinal cord, and nervous tissue of cattle—with cattle manure. The temporal and spatial distributions of CO₂, CH₄, and NH₃ emissions were measured in both zones. The gas generated in the aerobic and anaerobic zones and the unused supplied air were collected through an outlet and measured as cumulative gas emissions. The study examined the influence of SRM content (10, 20, and 30%), manure type, manure content, and phosphogypsum (PG, 16%) on gas emissions and carbon loss. All manures originated from cattle but differed in carbon (C) and nitrogen (N) content. Variations in pH, nitrogen-15 isotope (δ¹⁵N), nitrate ions (NO₃⁻), and ammonium ions (NH₄⁺) during the co-composting process were determined and discussed. Results indicated that anaerobic activity was minimized at 10% SRM but increased with higher SRM contents, while aerobic bacteria showed consistent responses across SRM levels of 10–30%. However, SRM consumption rates were influenced by manure type. Co-composting with 10% SRM produces 17.4 and 71.6% less CH₄ compared to 0 and 30% SRM, respectively, indicating that SRM content should be maintained at 10% to minimize CH₄ production. Adding 16% PG to pure manure and manure with 30% SRM can reduce NH₃ emissions by 75.8 and 98.1%, respectively, demonstrating that PG is considerably more effective when SRM is included.</p> Graphical Abstract <p></p>