The study aimed to investigate the efficacy of Pseudomonas fluorescens and Paenibacillus polymyxa as bioagents, along with the chemical systemic resistance inducers, i.e., hydroquinone (HQ) and benzoic acid (BA) individually and in combinations, to combat root rot and wilt diseases with promoting the growth of soybean plants. Pathogenicity tests have provided that all isolates could infect soybean cv. Giza 111, resulting in varying degrees of infection. The isolates of Rhizoctonia solani No. 3 with accession No. (OR975921.1) and Fusarium oxysporum No. 2 with accession No. (OR975922.1) were the most aggressive. In vitro, P. polymyxa combined with HQ showed the most effective in decreasing the fungal growth of both the examined fungi. In vivo trials conducted in pots and fields revealed that P. polymyxa + HQ treatment ranked just behind the Topsin M-70^® fungicide in terms of effectiveness. Anatomically, light microscope cross-sections of the primary roots revealed that the combinations of these agents led to protecting soybean plants from the harmful anatomical changes of both pathogens in the epidermis, cortex, and vascular cylinder structure under artificial infestation with the tested fungi. Physiological analyses indicated increased levels of peroxidase (PO) and polyphenoloxidase (PPO), along with total phenolic content (TPC), in plants treated with the combined agents compared to those treated individually. The combination treatments significantly enhanced plant growth metrics and yield components in field studies. Generally, results indicate that combining bioagents with chemical inducers proved more effective than individual applications and might be included in integrated disease management approaches.