Many studies have confirmed the validity of plant cover and organic farming in ameliorating soil quality. The goal of this study was to investigate the efficiency of rehabilitation practices in a degraded soil ecosystem consisting of: (i) organic or inorganic fertilization; and (ii) presence or absence of almond trees. The experiments were carried out for 2 years in the South of Italy in three fields characterized by different slope (0%, 2%, and 6%). Each field was split up into two parts, one assigned to organic fertilization and the other assigned to mineral fertilization, and planted with almond trees using GF677 or Franco rootstocks. The results showed that the organic fertilization, particularly in the presence of the Franco rootstock, resulted more effective in increasing soil organic matter content and microbial activity especially in the 0% and 2% slopes. However, in the 6% slope, where a lower soil metabolism was observed, an improvement of chemical and biochemical soil properties was generally evident for both fertilization systems. The Franco rootstock improved soil quality and maintaining a good production, whereas the GF677 has exploited more soil resources, resulting in a higher growth and yield; therefore, the use of almond tree with Franco rootstock associated with organic matter application is a useful practice in order to preserve soil quality and to rehabilitate degraded soils.