Aims: Acidification with concentrated H2SO4 is a novel strategy to reduce NH3 emissions from livestock slurry. It was recently found that also CH4 emissions from acidified slurry are reduced. This study investigated the microbiological basis and temporal stability of these effects. Methods and Results: Pig slurry from two farms, acidified by different techniques or untreated, was stored for 83 days in a pilot-scale facility. Methanogens were characterized before and after storage by T-RFLP and qPCR targeting mcrA. Emissions of NH3 and CH4 during storage were quantified. Acidified slurry pH was nearly constant at values of 5.5 and 6.5. Ammonia losses were reduced by 84 and 49%, respectively, while CH4 emission with both acidification techniques was reduced by >90%. T-RFLP fingerprints showed little effect of acidification or storage time. A major T-RF of 105 bp could represent methanogens related to Thermoplasmata (Tp). No treatment effects on gene copy numbers were seen with universal methanogen primers, whereas effects were found with Tp-specific primers. Conclusion: Methane emissions were reduced >90% during storage. Thermoplasmata-related methanogens could be involved in CH4 emissions from pig slurry. Significance and Impact of the Study: The effect of acidification on CH4 emissions during storage of pig slurry was quantified for the first time. Acidification with sulphuric acid holds promise as a novel greenhouse gas mitigation strategy for confined livestock production.