In sub-Saharan Africa, cattle manure is a critical yet undervalued bioresource, typically stored in uncovered heaps prior to land application, resulting in substantial greenhouse gas (GHG) emissions and nitrogen (N) losses. We quantified N losses and GHG emissions from six manure management treatments: uncovered and covered manure, interacted with or without straw or charcoal amendments. Covered manure treatments were sheltered with small roofs made of opaque polyethylene installed 10 cm above the container, while the uncovered treatments remained open. Aliquots of 200 kg solid cattle manure were incubated outdoors in open containers to simulate representative storage conditions. While charcoal addition reduced CH4 emissions, it did not affect N2O. Conversely, straw-amended treatments emitted approximately twice as much N2O as unamended manure, with no significant effect of covering. Site-specific 15N-N2O analysis provided evidence that denitrification dominated N2O production, with 85–95% of N2O reduced to N2. Emission factors ranged between 2.1 and 4.8% for N2O and 18.6-68.0 g CH4 kg−1 volatile solids, significantly exceeding IPCC default values, highlighting a critical gap in regional emission inventories. Overall, while straw amendment resulted in the greatest N losses, covering was an effective, low-cost and scalable option to preserve nutrients for sustainable crop production.