The international 4 per 1000 initiative aims at supporting states and non-governmental stakeholders in their efforts towards a better management of soil carbon (C) stocks. These stocks depend on soil C inputs and outputs. They are the result of fine spatial scale interconnected mechanisms, which stabilise/destabilise organic matter-borne C. Since 2016, the CarboSMS consortium federates French researchers working on these mechanisms and their effects on C stocks in a local and global change setting (land use, agricultural practices, climatic and soil conditions, etc.). This article is a synthesis of this consortium’s first seminar. In the first part, we present recent advances in the understanding of soil C stabilisation mechanisms comprising biotic and abiotic processes, which occur concomitantly and interact. Soil organic C stocks are altered by biotic activities of plants (the main source of C through litter and root systems), microorganisms (fungi and bacteria) and ‘ecosystem engineers’ (earthworms, termites, ants). In the meantime, abiotic processes related to the soil-physical structure, porosity and mineral fraction also modify these stocks. In the second part, we show how agricultural practices affect soil C stocks. By acting on both biotic and abiotic mechanisms, land use and management practices (choice of plant species and density, plant residue exports, amendments, fertilisation, tillage, etc.) drive soil spatiotemporal organic inputs and organic matter sensitivity to mineralisation. Interaction between the different mechanisms and their effects on C stocks are revealed by meta-analyses and long-term field studies. The third part addresses upscaling issues. This is a cause for major concern since soil organic C stabilisation mechanisms are most often studied at fine spatial scales (mm–μm) under controlled conditions, while agricultural practices are implemented at the plot scale. We discuss some proxies and models describing specific mechanisms and their action in different soil and climatic contexts and show how they should be taken into account in large scale models, to improve change predictions in soil C stocks. Finally, this literature review highlights some future research prospects geared towards preserving or even increasing C stocks, our focus being put on the mechanisms, the effects of agricultural practices on them and C stock prediction models.