Tannery wastewater is a major environmental pollutant that introduces toxic compounds, including chromium (Cr), into agricultural soils, posing significant challenges to plant growth and productivity. This research uniquely evaluates the efficacy of three specific plant growth-promoting rhizobacteria (PGPR)—Paenibacillus polymyxa, Bacillus amyloliquefaciens, and Pseudomonas putida—for mitigating Cr stress in rice (Oryza sativa L.). In this study, O. sativa plants were exposed to different levels of tannery wastewater (0%, 50%, and 100%) in a controlled pot experiment to assess the impact of P. polymyxa, B. amyloliquefaciens and P. putida on various morpho-physio-biochemical traits. Results from the present study revealed that the Cr toxicity induced a substantial decrease in shoot length, root length, number of leaves, leaf area, shoot fresh weight, root fresh weight, shoot dry weight, root dry weight, chlorophyll-a, chlorophyll-b, total chlorophyll, carotenoid content, net photosynthesis, stomatal conductance, transpiration rate, soluble sugar, reducing sugar, non-reducing sugar contents, calcium (Ca²⁺), magnesium (Mg²⁺), iron (Fe²⁺), and phosphorus (P) contents in the plants. However, Cr stress also induced oxidative stress in the plants by increasing malondialdehyde (MDA) and hydrogen peroxide (H₂O₂), which also led to an increase in various enzymatic and nonenzymatic antioxidants and also the gene expression and sugar content. Furthermore, a significant (P < 0.05) increase in proline metabolism, the AsA–GSH cycle, and the pigmentation of cellular components was observed. Addition of P. polymyxa, B. amyloliquefaciens and P. putide into the soil significantly alleviated Cr toxicity effects on O. sativa by improving photosynthetic capacity and ultimately plant growth. Increased activities of antioxidant enzymes in organic acid and PGPRs-treated plants seem to play a role in capturing stress-induced reactive oxygen species as was evident from lower levels of MDA and H₂O₂. Moreover, the application of different PGPRs enhanced both the abundance and diversity of the rhizosphere microbiome, with bacterial population levels and Shannon diversity indices significantly increasing. A marked reduction in daily Cr intake and associated health risks was also observed under these treatments, and proteomic responses under Cr stress. Research findings, therefore, suggested that the application of PGPRs can ameliorate Cr toxicity in O. sativa seedlings and resulted in improved plant growth and composition under metal stress.