This study investigated the effectiveness of two plant growth-promoting rhizobacteria (PGPR) formulations, Bio Arc® 6% WP (BA, Bacillus megaterium) and BECTO Grow Roots® (BGR; Serratia marcescens, Pseudomonas putida, and P. fluorescens). Additionally, it focused on naturally infested soil that had undergone metam potassium fumigation to reduce root-knot nematode (RKN), specifically Meloidogyne incognita. It aimed to monitor eggplant response to soil biodiversity changes for 60 days of the experiment under greenhouse conditions. Our data showed that soil fumigation eliminated nematodes and reduced other microorganisms significantly. In sterilized soil, plant fresh root weight significantly decreased after the elimination of soil biota. Moreover, BGR achieved the highest plant growth vigor [fresh root (18.48%), fresh shoot (23.52%), and fresh plant weight (21.03%)], followed by BA [fresh root (11.98%), fresh shoot (20.77%), and fresh plant weight (16.38%), respectively]. Plant growth traits increased significantly following the second reinoculation of PGPR after a month. Also, the same data trend was observed in treatments inoculated with RKN + PGPR. Furthermore, BGR treatments exhibited consistent efficacy in controlling nematode infection, maintaining superior vegetative growth compared to BA treatments over time. However, BA treatments displayed a decline in plant growth when faced with repeated nematode infection. The range of gall, egg mass, and second-stage juvenile (J2s) numbers diminished after inoculation-infected plants with RKN and PGPR compared with infected plants alone. Biochemical changes in eggplant roots cultivated in sterilized soil exposed significant enhancement in total sugars, protein, and nonenzymatic antioxidants (flavonoids and phenolic content), with antioxidant activity enhanced upon inoculation of PGPR and RKN. Oppositely, the levels of enzymatic antioxidants (catalase, peroxidase, and superoxide dismutase) decreased significantly with single and double PGPR application. However, the decline was less pronounced in the BGR treatments than in BA. In contradiction of oxidative enzymes, reinoculated PGPR + RKN multiplied significantly in reinfested RKN treatments. Our findings support the use of PGPR combinations, in particular, for preventive inoculation against M. incognita. They also enhance plant growth-promoting factors and stimulate plant defenses against inevitable soil reinfestation following soil fumigation.