Greenhouse gas and ammonia emissions from organic and mineral fertilizer application in agriculture contribute significantly to ecosystem eutrophication and global warming. To reduce ammonia emissions from slurry, acidification using sulfuric acid is one of the most effective practices, but the costs for machinery as well as requirements concerning environmental and labour safety are a challenge for small farms. For this reason, there is a rising interest in sustainable and cost-effective alternative slurry amendments, particularly bio-acidification and mineral amendments. Research on the subject has focused primarily on reducing ammonia and greenhouse gas emissions during slurry storage, leaving the impact on emissions following fertilizer application to soil-plant systems largely unexplored. Therefore, this study evaluates the effect of the three different slurry amendments cheese whey, sauerkraut juice, and leonardite on ammonia, nitric oxide, and greenhouse gas (methane, nitrous oxide, carbon dioxide) emissions from soil-plant mesocosms. After slurry application, emissions were measured for nine days using an automated incubation system and mesocosms received 80 kg N ha-1 untreated slurry or a mixture of slurry and amendment. Amending slurry with cheese whey significantly reduced ammonia emissions by 91 % and nitrous oxide by 23 %. Sauerkraut juice significantly decreased ammonia emissions by 92 % but significantly increased nitrous oxide emissions compared to slurry treatment. Leonardite reduced ammonia and nitrous oxide emissions insignificantly. These findings suggest that bio-acidification of slurry using cheese whey or sauerkraut juice is the most effective method for reducing ammonia emissions following fertilizer application in soil-plant mesocosms. A large variability particularly of nitrous oxide, nitric oxide and ammonia emissions from soil cores receiving unamended fertilizer indicated the importance of field-scale experiments to further verify the findings at larger scales and at natural soil environmental conditions.