Stevia rebaudiana is associated with the production of calorie-free steviol glycosides (SGs) sweetener, receiving worldwide interest as a sugar substitute for people with metabolic disorders. The aim of this investigation is to show the promising role of endophytic bacterial strains isolated from Stevia rebaudiana Egy1 leaves as a biofertilizer integrated with Azospirillum brasilense ATCC 29,145 and gibberellic acid (GA3) to improve another variety of stevia (S. rebaudiana Shou-2) growth, bioactive compound production, expression of SGs involved genes, and stevioside content. Endophytic bacteria isolated from S. rebaudiana Egy1 leaves were molecularly identified and assessed in vitro for plant growth promoting (PGP) traits. Isolated strains Bacillus licheniformis SrAM2, Bacillus paralicheniformis SrAM3 and Bacillus paramycoides SrAM4 with accession numbers MT066091, MW042693 and MT066092, respectively, induced notable variations in the majority of PGP traits production. B. licheniformis SrAM2 revealed the most phytohormones and hydrogen cyanide (HCN) production, while B. paralicheniformis SrAM3 was the most in exopolysaccharides (EPS) and ammonia production 290.96 ± 10.08 mg/l and 88.92 ± 2.96 mg/ml, respectively. Treated plants significantly increased in performance, and the dual treatment T7 (B. paramycoides SrAM4 + A. brasilense) exhibited the highest improvement in shoot and root length by 200% and 146.7%, respectively. On the other hand, T11 (Bacillus cereus SrAM1 + B. licheniformis SrAM2 + B. paralicheniformis SrAM3 + B. paramycoides SrAM4 + A. brasilense + GA3) showed the most elevation in number of leaves, total soluble sugars (TSS), and up-regulation in the expression of the four genes ent-KO, UGT85C2, UGT74G1 and UGT76G1 at 2.7, 3.3, 3.4 and 3.7, respectively. In High-Performance Liquid Chromatography (HPLC) analysis, stevioside content showed a progressive increase in all tested samples but the maximum was exhibited by dual and co-inoculations at 264.37% and 289.05%, respectively. It has been concluded that the PGP endophytes associated with S. rebaudiana leaves improved growth and SGs production, implying the usability of these strains as prospective tools to improve important crop production individually or in consortium.