Recent studies consider the native flora as a potential source of plant candidates for phytostabilization of metal and metalloid (MM) contaminated soils, but ecological restoration is not the main objective of these researches. However, in contaminated areas, phytostabilization should be considered as a useful tool for ecological restoration. The present study takes stock of 3 years of a Mediterranean pilot site implementation using native plant species to recover plant and microbial communities (diversity and functions) together with soil re-mediation in the Calanques National Park. To determine the success of this operation, three in situ treatments were compared: ecological restoration plots characterized by the handling of physical environment (creation of cultivation terraces) and plants, negative control plots without vegetation but with the same physical environment handling as ecological restoration plots, and positive control plots with natural vegetation and no handling. The results suggest that an ecological restoration trajectory is initiated in the ecological restoration plots, characterized by a partial permanent plant cover. However, there is no evidence of a significant improvement of soil quality (evaluated by soil texture, pH, nutrients and organic carbon contents, cation exchange capacity, microbial biomass and activities) and phytostabilization efficiency after 3 years. Native plant communities and their associated microorganisms may need more time before improving soil quality and MM stabilization under the drastic Mediterranean conditions. Any amendment addition to accelerate restoration and MM immobilization was forbidden in this protected area. Under such conditions, an active restoration need to be carried out in this contaminated area even if resilient dynamics of the native plant communities may sporadically occur over a long period of time.