Given the current degradation problems that Mediterranean soils endure, the implementation of alley cropping in olive orchards has been suggested as a sustainable strategy to increase agricultural productivity and improve carbon storage and soil fertility. Therefore, the objective of this study was to evaluate in the short term (3 years) the effect of alley cropping with minimum tillage versus conventional tillage in a traditional rainfed olive grove on soil organic carbon, total nitrogen concentrations, and stocks. Changes in soil quality through a stratification index, and the success of the 4‰ strategy in these soils with this type of management were also evaluated. Three intercropping strategies were tested: Crocus sativus (D-S), Vicia sativa and Avena sativa in rotation (D-O), and Lavandula x intermedia (D-L), all with minimum tillage versus olive with conventional tillage without intercropping, which was used as a control. Intercropping increased soil organic carbon in topsoil (0–10 cm) by 41.1, 28.5, and 30.5% for D-S, D-O, and D-L, respectively, compared to conventional tillage. At a depth of 10–30 cm, the soil organic carbon and the soil organic carbon stock increased slightly, although significant differences were found only in D-L. In the diversified plots, total nitrogen did not vary. However, total nitrogen increased in olive with conventional tillage due to fertilisation. Concerning soil quality, no significant differences were observed when evaluating the soil carbon and nitrogen stratification index in any of the treatments. However, the implementation of intercropping reached the objectives set by the 4‰ initiative in these soils with an increase in soil carbon per hectare and per year of 80, 87.4, and 86.4% for D-S, D-O, and D-L, respectively. Therefore, based on these results, in the short term, intercropping treatment enhances carbon storage in these soils, effectively achieving the objectives of the 4‰ initiative.