Continuous aerobic treatment can be a mean to stabilize the nitrogen compounds in the manure or create condition for denitrification and removal of N under the form of di-nitrogen gas (N2). Aeration treatment of 3 days of less results in stabilization of the nitrogen by bounding up in the organic form. Nitrification will occur after 3 days or more and most of all the ammoniacal nitrogen (NH3, NH4) is than converted to nitrite/nitrate (NO2/NO3). With low aeration rates or with period where the aeration is stopped, denitrification will occur and up to 70% of the original N in the manure can be lost through N2 and N2O gas emissions. When the aeration is done at high temperature (50-60 C, thermophilic treatment), nitrogen losses can be done under the form of ammonia as nitrification is inhibited.

Aeration can be a mean to stabilize the nitrogen compounds (lower the possible ammonia emissions)to slower release organic forms. For longer aeration, denitrification can remove N and help in the situation where N is in excess. However, some manure nutrients other than N can than be the limiting factor.