Atractylis serratuloides is an abundant native spiny species that grows in the surroundings of superphosphate factories in Tunisia. This plant species is adapted to arid environments and tolerates a high level of fluoride pollution in soils. The aim of this study was to better understand the physiological mechanisms of fluoride tolerance of this species, comparing the fluoride-contaminated sites of Gabes and Skhira with the reference site of Smara. Results demonstrated the involvement of leaf element and phytometabolite balances in the in situ response of A. serrulatoides to fluoride. Calcium, sulphur and magnesium were differently distributed between the sites of Gabes and Smara in all plant organs. No specific tissue fluorine accumulation in root, stem and leaf, even in the most contaminated site at Gabes, was detected by EDAX mapping. Lower anthocyan and flavonol levels but enhanced nitrogen balance index were found in A. serrulatoides leaves from Gabes compared to the two other sites. A. serratuloides appeared as a fluoride excluder and its tolerance involved calcium interactions with fluoride. Moreover, an occurrence of dark septate endophytes and arbuscular mycorhizal fungi in root systems of A. serratuloides was reported for the first time, and these symbioses were present but low at all sites. We suggest the use of this plant species for fluoride-polluted soil stabilization.