Urgent action is needed to ensure humanity’s future under climate change. Agriculture faces major challenges as it is both influenced by and contributes to climate change. Conservation agriculture sequesters carbon (C) in the soil due to practices such as reduced tillage and planting of cover crops. This study assessed effects of an innovative conservation agriculture popcorn (Zea mays) and wheat (Triticum aestivum) crop rotation in south-western France on soil C sequestration, GHG emissions and several environmental impacts. Two complementary approaches were used: i) a comparison based on field data and expert judgement to assess short-term effects and ii) modelling of three scenarios to quantify long-term outcomes. In both approaches Life cycle assessment (LCA) was used to compare popcorn and wheat rotations. The conventional rotation used ploughing, and its soil was bare between wheat harvest and popcorn sowing. Conservation agriculture used reduced tillage, cover crops, and compost of green waste. Impacts of compost production were allocated mainly to its waste treatment function, based on waste treatment cost and compost price. Simulation modelling of soil C was used to estimate the amount of C sequestered by the conservation and conventional crop rotations. LCA was combined with soil C modelling over 100 years to assess the long-term climate change impact of three scenarios for the popcorn and wheat rotation. These scenarios were 1) Conventional agriculture, 2) Conservation agriculture with cover crops only, 3) Conservation agriculture with cover crops + compost. Mean annual C sequestration and net climate change impact were -0.24 t/ha and 3867 kg CO2-eq./ha, respectively, for the conventional rotation and 0.91 t/ha and 434 kg CO2-eq./ha, respectively, for the conservation rotation. The climate change impact of the conservation rotation depended strongly on the allocation of composting impacts between the waste treatment and compost production functions. Compared to the conventional rotation, the conservation rotation had a lower marine eutrophication impact (-7%) but higher impacts for terrestrial acidification (+9%), land competition (+3%), and cumulative energy demand (+2%). Modelling over 100 years revealed that, at near soil C equilibrium, a conventional scenario lost 9% of soil C, whereas conservation agriculture scenarios gained 14% (only cover crop) and 26% of soil C (cover crop + compost). Conservation agriculture resulted in soil C sequestration over several decades, until a new soil C equilibrium was reached.