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The oasis soils of Tunisia face several climatic and soil constraints. Trying to have cultures that are profitable and beneficial in terms of soil C and N sequestration in such environments is already a challenge. To conduct this, we tested under identical conditions four types of occupation in sub-plots adjacent to the crops; barley alone, alfalfa alone, intercropping barley/alfalfa, and a control fallow in a saline gypseous desert soil poor in organic matter. Field experimentation was carried out in the oasis of Degache, which is very representative of other Tunisian oases. The stocks of C and N of the plot were calculated from the start in September 2019 before the installation of the different crops. After 21 months, the control plot shows a decrease of −41% in its stock of C and −25% in its stock N. However, the best result is that of the barley/alfalfa intercropping with an increase of +126.46% in the C stock and +178.67% in the N stock. After almost two years of experience, the beneficial effect of the intercropping system in the oasis is clear. These results are very motivating and seem to be a solution to the rapid decline in soil organic stocks.