Background: Application nano iron chelate and AMF fertilizer can increase plants' tolerance against water deficit stress. The main objectives of the current study were to investigate the effect of arbuscular mycorrhizal fungi (AMF) and nano iron chelate fertilizer under drought stress on grain yield, leaf chlorophyll contents, root colonization, oil percentage, and fatty acids profile of Lallemantia species. The experiment was carried out as a factorial based on a complete randomized block design consisting of three factors of irrigation levels of 90 (I90), 60 (I60), and 30% (I30) depletion of available soil water (ASW)), fertilizer levels of control (no fertilizer), AMF inoculation, and nano iron chelate, and plant species of Lallemantia (L. iberica and L. royleana) at the Research Farm of College of Agriculture, Shahed University, Tehran, Iran, in 2018/2019. Results: The results showed that increasing water deficit stress significantly decreased the above traits while applying nano iron and AMF fertilizers significantly increased them across water treatments. AMF fertilizer inoculation significantly improved both species yield. Higher root colonization by AMF inoculation enhanced seed oil and fatty acids (palmitic acid, stearic acid, oleic acid, linoleic acid, linolenic acid, arachidic acid, and Eicosenoic acid). In contrast, applying nano iron chelate by increasing chlorophyll content in any irrigation regime could enhance seed oil and some fatty acids such as palmitoleic acid. Conclusions: Water deficit stress and application of fertilizers had different effects on both species. L. iberica, compared to L. royleana, had the most tolerance to water deficit stress and the highest dependence on AMF inoculation. Overall, these results demonstrated that the application of AMF could improve major features of Lallemantia species under deficit irrigation conditions, especially at the I60 irrigation level.