The tomato is a widely cultivated and consumed vegetable globally. Comarca Lagunera is an important tomato-exporting region of Mexico. Salinity is an abiotic factor that reduces productivity and increases production costs. To advance growing period, there is high demand for the sustainable production of seedlings. Plant-growth-promoting rhizobacteria (PGPR) are characterized by improving plant growth through different mechanisms and can be an option for reducing the misuse of chemical fertilizers. The importance of the application of strains, evaluating various inoculation methods (in seed, soil, foliar spraying, and root immersion), should be evaluated to propose biofertilization packages in a specific crop. Thus, the study aimed to determine the effect of PGPR (Bacillus paralicheniformis, Acinetobacter guillouiae, Aeromonas caviae, and Pseudomonas lini) vs. nutrient solution and distilled water in the seedlings stage of saladette-type tomato on morphophysiological variables, nitrate reductase (NR) enzyme activity, and plant minerals via tissue analysis under greenhouse conditions. The four PGPR were inoculated by different methods (inoculation in seed, sprinkling, and both) in saladette-type tomato seedlings under greenhouse conditions and evaluated in vivo 40 days after sowing for morphophysiological variables, such as seedling height; stem diameter; root displaced volume; fresh and dry weight matter of the leaves, stems, and roots; leaf area; and nitrate reductase enzyme activity. The effect of the inoculation of PGPR showed significant results for Pseudomonas lini vs. the control, with 40% higher values, on average, for plant height, stem diameter, displaced root volume, and fresh weight of root, leaf, and stem. The response of enzymatic and mineral content in seedlings was variable with nutrient solution and significant with distilled water. Studies related to the promotion of plants in the subsequent phenological stages of a tomato, considering the selected PGPR, should be considered in future research.