Organic fertilization can preserve soil organic matter (SOM) and is foreseen as an effective strategy to reduce green house gases (GHGs) emissions in agriculture. However, its effectiveness needs to be clarified under specific climate, crop management and soil characteristics. A field experiment was carried out in a Mediterranean drip irrigated maize system to assess the pattern of soil CO2 and N2O fluxes in response to the replacement of a typical bare fallow–maize cycle under urea fertilization (130 kg N ha−1 y−1) (CONV) with: (i) bare fallow-maize cycles under two doses of compost (COM1 and COM2, 130 and 260 kg N ha−1 y−1, respectively) and (ii) a vetch-maize cycle, with vetch incorporation as green manure (130 kg N ha−1 y−1) (GMAN).Along the maize period (MP), reduced daily N2O emissions were detected in organic treated soils compared to CONV, mainly in the first stages of the cultivation, thanks to the slow release of available nitrogen from the organic substrates. Cumulative N2O fluxes (kg N2O-N ha−1) in MP scored to 0.24, 0.14, 0.12 and 0.085 for CONV, COM1, COM2 and GMAN, respectively, with significantly lower emissions in GMAN respect to CONV. CO2 fluxes partially reflected the ranking observed for maize yields, with cumulated values (Mg CO2-C ha−1) of 2.2, 1.5, 2.1, 2.1 for CONV, COM1, COM2 and GMAN, respectively, and significantly lower in COM1 respect to the other treatments.During the fallow period (FP), compared to CONV (0.77 Mg CO2-C ha−1 and 0.25 kg N2O-N ha−1), enhanced GHG fluxes were detected in COM treatments (about 0.90 Mg CO2-C ha−1 and 0.37 kg N2O-N ha−1, as averaged values from COM1 and COM2), likely driven by the slow prolonged mineralization of the added organic matter. GMAN showed comparable CO2 (0.82 Mg CO2-C ha−1) and N2O emissions (0.30 kg N2O-N ha−1), in consequence of restrained post-harvest residual N coupled with the counteracting effect of vetch uptake.Respect to the total yearly GHG emissions in CONV (about 194 kg CO2 eq ha−1 y−1), the overall results showed commensurate slightly higher GWP in COM treatments (+11% as averaged value from COM1 and COM2). The yield-scaled global warming potential (GWP) resulted 60% higher and nearly doubled for COM2 and COM1 respectively, according to the lower COM yields, markedly dampening at halved compost dose. GMAN appeared the best performing organic treatment, with lower GWP (−27%) and competitive yields respect to CONV.All treatments showed N2O emission factors consistently lower compared with the default IPCC 1% value.