Field emissions of greenhouse gases and also ammonia account for a large part of total Flemish agricultural emission. Further knowledge build-up and transfer are necessary to provide farmers with measures to reduce these emissions and the related environmental impact. A first objective is to derive regional emission factors for nitrous oxide and ammonia from empirical research. A second objective is to provide options for mitigation through fertilizer management. A third goal is to determine the greenhouse gas balance of carbon sequestration management. Next to this applied component, the research is also fundamental in nature. Goals are the mechanistic unraveling of how stabilization of organic matter occurs in soils, how conversion of subsurface plant C inputs to organic matter occurs and what interaction exists with soil structure in the process. This knowledge will be used to improve biogeochemical models for prediction of emissions as a function of climate and management.