The present study was conducted aiming at the protection of the shallot (Allium altissimum Regal) in natural habitat, which is endangered due to excessive harvesting. In order to increase the sustainability of this product, its wild ecotypes were planted in agricultural land and the effect of bio-fertilizers (nitroxin and phosphate) and sulfur on quantitative (yield and yield components) and qualitative (the active ingredient, allicin, crude protein, and the amount of phosphorus and potassium) traits were investigated. The results showed that the amount of allicin, crude protein, phosphorus, potassium, and yield in the planted ecotypes were significantly higher than the wild type in the studied natural habitat. The results of this study indicated a significant difference respecting quantitative and qualitative trait of cultivated shallot with proper nutritional management compared to wild shallot. Therefore, the expansion and development of this method can lead to the sustainability of the production of shallot and will conserve diversity of its populations in natural habitat.