Animal manure contributes considerably to ammonia (NH3) and greenhouse gas (GHG) emissions in Europe. Various treatment technologies have been implemented to reduce emissions and to facilitate its use as fertilizer, but a systematic analysis of these technologies has not yet been carried out. This study presents an integrated assessment of manure treatment effects on NH3, nitrous oxide (N2O) and methane (CH4) emissions from manure management chains in all countries of EU-27 in 2010 using the MITERRA-Europe model. Effects of implementing 12 treatment technologies on emissions and nutrient recovery were further explored through scenario analyses; the level of implementation corresponded to levels currently achieved by forerunner countries. Manure treatment decreased GHG emissions from manures in EU countries by 0-17% in 2010, with the largest contribution from anaerobic digestion; the effects on NH3 emissions were small. Scenario analyses indicate that increased use of slurry acidification, thermal drying, incineration and pyrolysis may decrease NH3 (9-11%) and GHG (11-18%) emissions; nitrification-denitrification treatment decreased NH3 emissions, but increased GHG emissions. The nitrogen recovery (% of nitrogen excreted in housings that is applied to land) would increase from a mean of 57% (in 2010) to 61% by acidification, but would decrease to 48% by incineration. Promoting optimized manure treatment technologies can greatly contribute to achieving NH3 and GHG emission targets set in EU environmental policies.