Brassicaceae products have been extensively studied for their biofumigant activity; despite this, few investigate their effect on soil proprieties. This paper aims to describe the effect on soil fertility by adding the seed meal of Brassica carinata at three different doses corresponding to field dose (3 tons/ha), 10 and 100 fold this dose in organic soil. The organic carbon balance was evaluated by analysing the oxidisable, humified and mineralised carbon fractions. Microbial activity was measured by enzymes linked to the carbon, phosphorous and sulphur cycles—β-glucosidase, phosphatase and arylsulphatase, respectively. The amount corresponding to 30 t/ha was the best solution for the mineralised carbon and humic carbon ratio. In contrast, there was a substantial increase in the organic substance’s mineralisation level at the maximum dose, not offset by a relative rise in humification. No repression was observed in the metabolic activity of the microorganisms, their abundance or the main enzymatic activities and, in the conditions tested, a release of only a volatile isothiocyanate occurred, limiting the biofumigant effect. Therefore, these combined factors allow us to assert that the amendment with this type of material at the intermediate dose could positively affect the phosphorus cycle, the soil structure, and fertility.