Most metal polluted natural environments are contaminated with multiple metals, and arbuscular mycorrhizal (AM) fungi are among the extracellular strategies to avoid metal toxicity. To understand the interaction between Cd, Zn and AM fungi Glomus mosseae, two genotypes (Sel 85N and P792) of pigeonpea (Cajanus cajan L. Millsp.), differing in their metal tolerance, were chosen for study. Results revealed that root dry weights were more severely affected than shoot dry weights as both the metals were accumulated in roots than in the aerial parts. Mycorrhization promoted biomass yields by decreasing metal content in plant tissues. Exposure to the metals resulted in oxidative burst (high H2O2, malondialdehyde contents and electrolyte leakage), which was accompanied by decreased membrane stability. However, increase in the level of total non‐protein thiols (TNP‐SH) and the activity of antioxidant enzymes like superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and glutathione reductase (GR) suggested that all these parameters were synergistic in combating heavy‐metal‐induced oxidative stress. Zn supplementation proved to be inhibitory for Cd‐induced oxidative stress. AM fungi alleviated oxidative stress through enhanced production of TNP‐SH as well as through upregulation of antioxidant enzymes. Sel 85N exhibited lesser oxidative damage and more efficient defence mechanism than P792.