The European Commission is directing efforts into triggering the storage of carbon in agricultural soils by encouraging the adoption of carbon farming practices under the European Green Deal and in other key EU policies. However, farmers that want to enter this production model urgently need to define the sustainable practices required for increasing soil organic carbon without overturning production systems and also need to adapt it for optimizing yields and improving carbon stocks. However, there is still a lack of tools that are easy to use and interpret for guiding farmers and stakeholders to find ways in which to increase soil organic carbon content. Therefore, this research aims to set up a novel bottom–up approach, in terms of the methodology and analysis process, for identifying tailored sustainable farming management strategies for the purpose of increasing soil carbon. We investigated 115 real food production cases that were carried out under homogeneous pedo-climatic conditions over a period of 20 years in the Apulia region (Southern Italy), which made it possible to create a dataset of 12 variables that were analyzed through a decision tree (created with the C4.5 algorithm). The overall results highlight that the treatment duration was the most crucial factor and affected the carbon stock both positively and negatively. This was followed by the use of cover crops alone and then those in combination with a type of irrigation system; hence, specific agricultural management strategies were successfully identified for obtaining effective carbon storage in the considered real food production cases. From a wider perspective, this research can serve as guidance to help EU private actors and public authorities to start carbon farming initiatives, pilot projects, or certification schemes at the local and/or regional levels.