Iron chlorosis in the calcareous soils is one most important stress factors worldwide that limits photosynthesis and decreases fruit yield and quality. Certain soil rhizobacteria produce organic compounds such as plant acids and they may reduce the soil rhizosphere pH and affect ferric chelate reductase (FC-R) activity in root. However, there is no knowledge regarding changes in organic acids content and FC-R activities of leaf due to rhizobacterial root inoculation. Therefore, the efficiency of six plant growth promoting rhizobacteria (PGPR) were tested on apple cv. Braeburn on M9 and MM106 rootstocks. The results of the experiment showed leaf organic acid contents, iron quantity of soil, root and leaf and root and leaf FC-R activity were significantly affected via rhizobacteria applications in apple plants. In MM106 and M9, there was a remarkable increase in Fe in M3 inoculated soil by 95 and 89%, respectively, compared to control. Average increases in citric, malic, malonic, butyric and lactic acid in the leaf were obtained from rhizobacterial root inoculations of 25.1, 21.8, 29.6, 18.0 and 18.2% in Braeburn/MM106, respectively. In Braeburn/M9, MFDCa1 application increased all organic acid concentrations compared to the control. MFDCa2 treatment caused the maximum leaf FC-R activity in Braeburn on M9 and MM106 (60.9 and 50.3 nmol Fe+2 g−1 FW h−1, respectively) while the least values were determined in the control (33.5 and 29.9 nmol Fe+2 g−1 FW h−1, respectively). This study showed the bacterial strains tested in our study may be used as a biofertilizer instead of Fe fertilizers.