Conservation agriculture that includes no tillage (NT) or minimum tillage (MT) and crop rotation is an effective practice to increase soil organic matter in Mediterranean semiarid agrosystems. But the impact of these agricultural practices on greenhouse gases (GHGs), such as nitrous oxide (N2O) and methane (CH4), is variable depending mainly on soil structure and short/long-term tillage. The main objective of this study was to assess the long-term effect of three tillage systems (NT, MT and conventional tillage (CT)) and land-covers (fallow/wheat) on the emissions of N2O and CH4 in a low N input agricultural system during one year. This was achieved by measuring crop yields, soil mineral N and dissolved organic C contents, and fluxes of N2O and CH4. Total cumulative N2O emissions were not significantly different (P > 0.05) among the tillage systems or between fallow and wheat The only difference was produced in spring, when N2O emissions were significantly higher (P < 0.05) in fallow than in wheat subplots, and NT reduced N2O emissions (P < 0.05) compared with MT and CT. Taking into account the water filled pore space (WFPS), both nitrification and denitrification could have occurred during the experimental period. Denitrification capacity in March was similar in all tillage systems, in spite of the higher DOC content maintained in the topsoil of NT. This could be due to the similar denitrifier densities, targeted by nirk copy numbers at that time. Cumulative CH4 fluxes resulted in small net uptake for all treatments, and no significant differences were found among tillage systems or between fallow and wheat land-covers. These results suggest that under a coarse-textured soil in low N agricultural systems, the impact of tillage on GHG is very low and that the fallow cycle within a crop rotation is not a useful strategy to reduce GHG emissions.