The response of a Petrocalcic Palexeroll dedicated to the cultivation of vegetables (Apium graveolens L.) with a rotation of a mixture of cereals and legumes when organic amendments are added has been studied; specifically, three fertilization treatments were experimented with: two organic (LSM and COA) and one with chemical fertilizers (I). The LSM and COA plots were managed according to the regulations governing organic production, while in I, conventional agricultural production practices were used. Over a three-year period, monthly samples were taken from the topsoil and analyzed for organic carbon (OC), total nitrogen (TN), C/N ratio, total P (P), electrical conductivity of the saturation extract (ECext) and extract ions, pH in water (pHw) and 1 M KCl (pHKCl), cation exchange capacity (CEC), exchangeable bases (Mg2+, K+, Na+), and assimilable elements (Fe, Cu, Mn, Zn). The results obtained indicated significant differences between the treatments for the OC, TN, C/N, and P; specifically, in the case of OC the mean concentrations were 22.2 > 20.1 > 17.5 g kg−1 for the LSM, COA, and I, respectively. The addition of organic amendments also improved the soil function for food production, evidenced by the higher concentrations of K, Mg, and micronutrients. The ECext and extracted ions were also sensitive to the treatments such that the sequence of ECext in the third year was COA = LSM > I, with values of 5.0, 4.8, and 3.3 dSm−1, which forced a rethink of the doses of the amendments applied. These results suggest that the LSM-based agronomic model had a beneficial effect on the soil properties and contributed to its function as a C sink.