Plant growth, grain yield, and the nutritional grain quality reduce in Zinc (Zn)-deficient soils. As a practical approach, the utilization of plant growth-promoting microorganisms offers a promising approach to cope with Zinc deficiency. This study was carried out to determine the effects of endophytic fungus Piriformospora indica and rhizobacterium Pseudomonas putida on growth, nutrient status, and antioxidant enzyme activities of two wheat (Triticum aestivum L.) genotypes under Zn deficiency. The experiment was conducted using a completely randomized factorial design with three replications and three treatments: wheat genotypes [Zn-efficient (H-Zn) genotype, Azadi and Zn-inefficient (L-Zn) genotype, Niknejad]), Zn concentrations (0 and 2 μmol Zn L−1) and microbial inoculations (P. indica and P. putida). Under Zn deficiency, P. indica, P. putida, and dual inoculation of P. indica with P. putida significantly increased the shoot dry weight of L-Zn genotype up to 10.3%, 25.6% and, 15.4% compared to control plants, respectively. Inoculation of P. indica led to an increase in thinner and highly-branched roots and subsequently increased Zn uptake in the shoot of L-Zn genotype under Zn deficiency. Under such condition, individual inoculation of L-Zn genotype with P. putida and P. indica increased peroxidase activity by 85.7% and 40% compared with non-inoculated plants. Malondialdehyde content of both wheat genotypes inoculated with P. indica was significantly decreased compared to the non-inoculated plants. Generally, depending on the wheat genotype, P. indica and P. putida can increase plant tolerance by affecting only part of the tolerance mechanisms (including antioxidant and non-antioxidant mechanisms) under Zn deficiency stress. In summary, P. indica and P. putida could improve the fitness of the L-Zn genotype under Zn-deficiency stress.