There is currently an intense debate about the potential for additional organic carbon storage in soil, the strategies by which it may be accomplished and what the actual benefits might be for agriculture and the climate. Controversy forms an essential part of the scientific process, but on the topic of soil carbon storage, it may confuse the agricultural community and the general public and may delay actions to fight climate change. In an attempt to shed light on this topic, the originality of this article lies in its intention to provide a balanced description of contradictory scientific opinions on soil carbon storage and to examine how the scientific community can support decision-making despite the controversy. In the first part, we review and attempt to reconcile conflicting views on the mechanisms controlling organic carbon dynamics in soil. We discuss the divergent opinions about chemical recalcitrance, the microbial or plant origin of persistent soil organic matter, the contribution of particulate organic matter to additional organic carbon storage in soil, and the spatial and energetic inaccessibility of soil organic matter to decomposers. In the second part, we examine the advantages and limitations of big data management and modeling, which are essential tools to link the latest scientific theories with the actions taken by stakeholders. Finally, we show how the analysis and discussion of controversies can guide scientists in supporting stakeholders for the design of (i) appropriate trade-offs for biomass use in agriculture and forestry and (ii) climate-smart management practices, keeping in mind their still unresolved effects on soil carbon storage.