Organic waste recycling in agriculture can enhance the efficiency of nutrient cycles and directly or indirectly reduce major and increasing sources of greenhouse gas emissions. It can also boost soil fertility and agricultural resilience to climate change. There is considerable potential for improving recycling that has been studied from the farm to the territorial scale. We present research results concerning the improvement and introduction of recycling practices on several scales and concerning associated biophysical processes allowing more reliable assessment of greenhouse gas emission balances. Whether concerning the resilience of agricultural systems or the mitigation of emissions, the agricultural waste recycling potential is highest on the territorial scale, especially when the spatial concentration of various wastes is high, e.g. in periurban areas around fast-growing megacities in developing countries. CIRAD has developed recycling management methods and support tools and is enhancing knowledge on processes that determine the climate footprint of recycling. The aim is to fill the many knowledge gaps regarding greenhouse gas emission factors and determinants of organic matter bioprocessing in tropical conditions.