Nutrient deficiencies in alkaline soils (pH 7.9–8.5) frequently limit plant growth due to insufficient nutrient availability and uptake. This study investigated the effects of two bacterial strains, VITK-1 and VITK-3, on nutrient absorption, growth, and gene expression in tomato (Solanum lycopersicum) seedlings grown in alkaline soil. Bacterial treatments were applied individually and as a consortium, and their ability to promote plant growth and nutrient solubility was evaluated. In vitro studies demonstrated the strains’ ability to solubilize essential nutrients, generate extracellular enzymes, and exhibit a variety of Plant Growth-Promoting Rhizobacteria (PGPR) characteristics, including soil-borne pathogen control. In vivo investigations revealed notable improvements in germination, root and shoot development, and overall seedling vigor when compared to untreated controls. The bacterial consortium significantly improved protein and proline levels, antioxidant activity, phenolic and flavonoid content, and decreased carbohydrate accumulation. Furthermore, treated plants exhibited activation of nutrient-regulating genes associated with better root metabolism and resilience to stress. These results show the potential of PGPR inoculants, particularly consortia, as a promising strategy for improving nutrient uptake, biochemical characteristics, and stress tolerance in crops grown in alkaline soils.