Twenty fluorescent Pseudomonas isolates were tested for their ability to produce siderophores on chrome azurol S (CAS) agar plates and their antagonistic activity against six plant pathogenic fungal isolates was assessed. Scaling-up production of siderophores from the promising isolates, P. aeruginosa F2 and P. fluorescens JY3 was performed using batch and exponential fed-batch fermentation. Finally, culture broth of the investigated bacterial isolates was used for the preparation of two economical bioformulations for controlling Fusarium oxysporum and Rhizoctonia solani. The results showed that both isolates yielded high siderophore production and they were more effective in inhibiting the mycelial growth of the tested fungi compared to the other bacterial isolates. Exponential fed-batch fermentation gave higher siderophore concentrations (estimated in 10 µL), which reached 67.05% at 46 h and 45.59% at 48 h for isolates F2 and JY3, respectively, than batch fermentation. Formulated P. aeruginosa F2 and P. fluorescens JY3 decreased the damping-off percentage caused by F. oxysporum with the same percentage (80%), while, the reduction in damping-off percentage caused by R. solani reached 87.49% and 62.5% for F2 and JY3, respectively. Furthermore, both formulations increased the fresh and dry weight of shoots and roots of wheat plants. In conclusion, bio-friendly formulations of siderophore-producing fluorescent Pseudomonas isolates can be used as biocontrol agents for controlling some plant fungal diseases.