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The necessity to decrease greenhouse gas (GHG) emissions, mainly methane (CH4), is underscored in diverse national and international regulations and conventions. Agriculture, particularly livestock enteric fermentation and manure management, is a significant source of these emissions. In pig and dairy cattle farming, liquid-manure systems are the most prevalent and responsible for an upsurge in CH4 emissions. This study further investigates the potential of CH4 production from manure as a renewable energy source and an effective strategy to decrease GHG emissions, emphasizing the importance of better understanding the factors that regulate CH4 potential loss from manure storage. This study scrutinized the effect of storage conditions and changes in chemical composition on CH4 formation and emissions from dairy and fattening pig manure. Two different experimental techniques were designed to verify the influence of storage temperature on CH4 production and the effects of manure storage on biochemical methane production (BMP). In the first method, samples were stored without inoculum at varying temperatures, and CH4 production was measured. In pig manure stored at 25°C and 20°C, CH4 production amounted to 69.3% and 50.3% of the BMP, respectively. The highest CH4 production for dairy slurry were observed at 25°C but remained low. The production of CH4 in dairy manure was found to be inhibited during storage. The study suggested several potential reasons for this inhibition, though further research is recommended to confirm these hypotheses. The second set of experiments, evaluate the BMP of manure samples collected year-round from different stages on the manure storage in dairy cow and fattening pig farms. The findings indicated a 20.5% reduction in the BMP of dairy manure due to alterations in chemical composition during the transfer from the barn to outdoor storage. Similarly, there was a 39.5% drop in the BMP for samples of fattening pig manure in the transition from intermediate to outdoor storage. When examining BMP relative to the age of the manure, it was observed that pig manure decomposes quicker than dairy manure. Mathematical models were developed to predict BMP from the chemical composition, and the most effective predictors for each livestock category were identified. Improvements to predict BMP for less aged samples with reduced variability in their chemical compositions would be necessary. Overall, this study highlights the necessity of promptly transporting manure to either a biogas plant or outdoor storage facilities. Such measures can help prevent significant CH4 emissions and avoid a decrease in energy production capacity.