Phosphate strip mining in Oron-Ziv region, Negev Desert, has been practiced for over 60 years, destroying the hyper-arid ecosystem, with its unique biodiversity, and fragmenting the landscape. In the last 15 years, a new method of reclamation-oriented mining is applied, where topsoil and overburden are piled separately and returned back in reverse order to maintain the main features of the original landscape. We study the ecological consequences of the new method using an ecosystem approach, to: (1) Analyze the differences in physical and biological groups (soil, microorganisms, plants, arthropods) between the natural (reference) and restored sites; (2) Propose additional practices to improve the reclamation success. We used a conceptual model to identify research directions and established research plots in four different sites to collect soil and monitor the focal biological groups. Soil analysis revealed that biological components differ significantly between natural and restored sits. Genetic analysis of the microbial community showed that the most crucial photosynthetic groups, e.g., cyanobacteria, are significantly less abundant in the restored compared with the natural sites, lessening the development of functional and stabilizing soil biocrusts. Using plant experiments, we showed that germination depression in the restored sites results from missing seed bank, probably because seeds do not accumulate in loose soil without biocrust. Additionally, the restored sites are characterized by generalist arthropods while the natural sites are inhabited by diverse specialist species. Our current studies focus on active practices that increase habitat heterogeneity and facilitate native biodiversity.