Soil fertilisation affects greenhouse gas emissions. The objective of this study was to compare the effect of different fertilisation strategies on N 2 O, CH 4 emissions and on ecosystem respiration (CO 2 emissions), during different periods of rice cultivation (rice crop, postharvest period, and seedling) under Mediterranean climate. Emissions were quantified weekly by the photoacoustic technique at two sites. At Site 1 (2011 and 2012), background treatments were 2 doses of chicken manure (CM): 90 and 170 kg NH 4 + -N ha − 1 (CM-90, CM-170), urea (U, 150 kg N ha − 1 ) and no-N (control). Fifty kilogram N ha − 1 ammonium sulphate (AS) were topdress applied to all of them. At Site 2 (2012), background treatments were 2 doses of pig slurry (PS): 91 and 152 kg NH 4 + -N ha − 1 (PS-91, PS-152) and ammonium sulphate (AS) at 120 kg NH 4 + -N ha − 1 and no-N (control). Sixty kilogram NH 4 + -N ha − 1 as AS were topdress applied to AS and PS-91. During seedling, global warming potential (GWP) was ~ 3.5–17% of that of the whole rice crop for the CM treatments. The postharvest period was a net sink for CH 4 , and CO 2 emissions only increased for the CM-170 treatment (up to 2 Mg CO 2 ha − 1 ). The GWP of the entire rice crop reached 17 Mg CO 2 -eq ha − 1 for U, and was 14 for CM-170, and 37 for CM-90. The application of PS at agronomic doses (~ 170 kg N ha − 1 ) allowed high yields (~ 7.4 Mg ha − 1 ), the control of GWP (~ 6.5 Mg CO 2 -eq ha − 1 ), and a 13% reduction in greenhouse gas intensity (GHGI) to 0.89 kg CO 2 -eq kg − 1 when compared to AS (1.02 kg CO 2 -eq kg − 1 ). [ABSTRACT FROM AUTHOR]