Globe artichoke is one of the most intensively cultivated horticultural species in Mediterranean regions. In this context, sustainable agronomic management is a requisite to increase the soil carbon content, making the artichoke cultivation system more resilient to climate change. A 10-year experiment was considered to forecast the influence on soil C dynamic of three globe artichoke managements: monoculture with dry crop residues incorporation (conventional monoculture), monoculture with the inclusion of a cover crop (alternative monoculture), and rotation with cauliflower plus cover crop (biannual rotation). During the 2006–2016 period, total soil organic carbon content and plant C inputs to soil were measured. RothC model was used to predict the effect on the soil C stock and C sequestration potential in 20 years of the three managements tested in the field, plus a hypothetical conventional scenario with no residues’ incorporation (no residues). Plant C inputs increased according to the number of crops in rotation in each system, resulting 25% lower in conventional monoculture with respect to biannual rotation, whereas the C stock change was significantly higher (p < 0.01) in conventional and alternative monoculture (+ 7.57 and 7.14 t C ha-1) compared to biannual rotation (-1.03 t C ha-1). In the 20-year predictions, all the systems had a positive C balance. The soil organic carbon change (t C ha-1) for the future climate was + 7.2 for alternative monoculture and + 0.6 for monoculture with residues removals. For the first time, in this study, we clearly shown in the long term and in a climate change perspective that an improper crop residues management might lead to a loss of soil fertility in intensively cultivated horticultural soils under Mediterranean climate. The adoption of biannual rotation with cauliflower needs to be evaluated carefully because it proved to be less efficient in terms of C sequestration potential.