Heavy metals induce negative impacts on plants, however, the symbiotic association of an arbuscular mycorrhizal fungi (AMF) Glomus fasciculatum offers an effective tolerance response. The aim of the present study was to investigate the impact of Lead (Pb), Arsenic (As), and Nickel (Ni) with and without the application of AMF on one of the important medicinal and aromatic plants Monarda citriodora Cerv. ex Lag (lemon beebalm). The metal concentrations mixed in soil were: Pb (25 and 50 mg/kg), As (15 and 30 mg/kg) and Ni (20 and 40 mg/kg) along with constant dose of AMF (2.7 g/kg soil) while untreated plants were taken for comparison. Results showed that higher concentrations of Pb (50 mg/kg), As (30 mg/kg), and Ni (40 mg/kg) decreased the plant height by 48%, 6%, and 7% respectively, and the number of branches by 19%, 10%, and 25% respectively when compared with controls. The biomass and nutrient contents were also altered in the plants that received Pb, As, and Ni. However, the application of AMF has improved the overall growth and development of plants but not more than the control. Furthermore, higher concentrations of Pb (50 mg/kg), As (30 mg/kg), and Ni (40 mg/kg) increased total phenolics by 975%, 375%, and 373% respectively, flavonoids by 149%, 136%, and 127% respectively, proline content by 656%, 225%, and 472% respectively, and radical scavenging activity by 124%, 146%, and 157% respectively, when compared with control. Additionally, higher concentrations of Pb, As, and Ni treatments also decreased the AMF colonization rate in roots by 37%, 35%, and 49% when compared with their lower concentrations. The elevation of secondary metabolites and scavenging activity in response to metal toxicity indicates that M. citriodora is a rich source of natural antioxidants. So, future strategies are required to study valuable antioxidant compounds present in this plant.