Liquid dairy manure storages emit large amounts of methane (CH4), nitrous oxide (N2O) and ammonia (NH3). Gradually filling manure storages is a standard practice, however, most studies have batch filling approaches. Gradual manure filling may emit different GHGs when inoculum is present, as it changes the substrate/microorganism ratio, manure temperature, and distribution of solids. This study compared CH4, N2O and NH3 emissions from gradually-filled and batch-filled 11.9 m3 capacity liquid dairy manure tanks with 0%, 10% or 20% inoculum over 122 day of storage. On average, gradually-filled tanks had 1.8 °C higher manure temperature, which may have contributed to a 12% increase in total CH4 emissions to 6.26 kg m−3 and 28% increase in total NH3 emissions to 328 g m−3. The absence of inoculum reduced CH4 emissions by 25% and 23% compared to the 10% inoculum tanks (6.48 kg m−3) and 20% inoculum tanks (6.31 kg m−3), respectively. Absence of inoculum had no effect on N2O and NH3 emissions. Gradual filling of tanks containing inoculum increased CH4 emissions by 27% to 7.38 kg m−3, while in the absence of inoculum CH4 emissions were reduced by 29% to 4.03 kg m−3. Our results suggest that research using inoculant in batch-filled manure storage systems may underestimate GHG emissions. Future research should further characterize the effects of gradual filling on solids and temperature profiles, and substrate availability linked to production of GHGs.