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The excess use of chemicals by farmers in the agroecosystems degrades soil quality, disturbs soil ecology, and increases soil salinity and health hazards in humans. <i>Stevia rebaudiana</i> is an important medicinal and aromatic crop whose leaves contain steviol glycosides (SGs). The <i>Bacillus safensis</i> NAIMCC-B-02323 strain STJP from the rhizosphere of <i>S. rebaudiana</i> producing salicylic acid (16.80 µg/mL), chitinase (75.58 U/mL), β-1,3-glucanase (220.36 U/mL), and cellulase (170 U/mL) was taken as a plant growth-promoting rhizobacteria (PGPR). The cell-free supernatant (CFS) from strain STJP showed significant biocontrol activity against <i>Alternaria alternata</i> (80%), suggesting the protective role of extracellular metabolite(s) against phytopathogens. Paneer whey-based bioformulation (P-WBF) was developed to exploit <i>B. safensis</i> STJP to enhance the growth, nutrient uptake, soil properties, stevioside content, and SGs biosynthesis in <i>S. rebaudiana</i> under an <i>A. alternata</i>-infested field. The combined treatment of P-WBF and mycorrhiza (<i>Glomus fasciculatum</i> ABTEC) significantly enhanced plant growth parameters after 90 days, in comparison with control. The symbiotic action (P-WBF and mycorrhiza) displayed much better results in terms of chlorophyll a and b (improved by 132.85% and 39.80%, respectively), protein (by 278.75%), flavonoid (by 86.99%), carbohydrate (by 103.84%), antioxidant (by 75.11%), and stevioside (by 120.62%) contents in plants as compared to the untreated set. Further, the augmentation of potassium (by 132.39%), phosphorous (by 94.22%), and zinc (by 111.11%) uptake in plant tissues and soil was also observed by the application of P-WBF and mycorrhiza. The expression of UGT74G1 and UGT85C2 genes related to SG biosynthesis was upregulated (2.7- and 3.2-fold, respectively) in plants treated with P-WBF and mycorrhiza as further confirmed by the accumulation of SGs. The results suggest that the application of P-WBF and mycorrhiza not only provides an ecofriendly and sustainable solution to improve stevioside content in <i>S. rebaudiana</i> by a nutrient-linked mechanism but also paves the way to enhanced production of stevioside.