In this study we estimated the emissions of NH3, CO2, N2O and CH4 from digestates subjected to a mechanical separation. NH3 and CO2 were the predominant N and C losses among those measured. Expressed on a CO2 equivalent basis, separation significantly increased GHG emissions for pig slurry, but not cattle slurry. Furthermore, it resulted in a significant reduction in NH3 emission potential (9 and 23% for pig and cattle, respectively) as estimated from the flux measurements.