Agriculture contributes to a significant proportion of global emissions of greenhouse gases (GHG) but can also participate in climate change mitigation. The introduction of legumes in crop rotations reduces the dependence on N fertilizers and may mitigate the carbon (C) footprint of cropping systems. The aim of this study was to quantify the C footprint of six low-input arable cropping systems resulting from the combination of three levels of grain legumes introduction in a 3-yr rotation (GL0: no grain legumes, GL1: 1 grain legume, GL2: 2 grain legumes) and the use of cover crops (CC) or bare fallow (BF) between cash crops, covering two rotation cycles (6¿years). The approach considered external emissions, on-site emissions and soil organic carbon (SOC) stock changes, and prioritized (i) field observations and (ii) simulation of non-measured variables with the STICS model, rather than default emission factors. As expected, fertilizers accounted for 80–90% of external emissions, being reduced by 50% and 102% with grain legumes introduction in GL1-BF and GL2-BF, compared to the cereal-based rotation (GL0-BF). Cover crops management increased machinery emissions by 24–35% compared to BF. Soil nitrous oxide (N2O) emissions were low, ranging between 205 and 333¿kg CO2 eq. ha-1¿yr-1 in GL1-BF and GL0-BF, respectively. Nitrate leaching represented the indirect emission of 11.6 to 27.2¿kg CO2 eq. ha-1¿yr-1 in the BF treatments and 8.2 to 10.7¿kg CO2 eq. ha-1¿yr-1 in the CC treatments. Indirect emissions due to ammonia volatilization ranged between 8.4 and 41.8¿kg CO2 eq. ha-1¿yr-1. The introduction of grain legumes strongly influenced SOC changes and, consequently, the C footprint. In the BF systems, grain legumes introduction in the rotations led to a significant increase in the C footprint, because of higher SOC losses. Contrarily, the use of cover crops mitigated SOC losses, and lowered the C footprint. These results indicated the need of CC when increasing the number of