Over-fertilization and agrochemicals adversely affect soil quality and agricultural ecosystem sustainability. Tomato (Solanum lycopersicum) is ranked as an important crop due to its high profitability and nutritional value. In Argentina, tomato is mainly produced in horticultural belts at peri-urban areas, whose soils frequently are contaminated by heavy metals and/or agrochemicals. To explore safer alternatives, we investigated the effects of seed inoculation with a common plant-growth-promoting rhizobacteria (PGPR), i.e., Bacillus subtilis subsp. spizizenii, on development at various growth stages of two tomato varieties, “Platense” and “Río Grande”, and on production and fruit quality at harvest time of the “Río Grande” variety. The experimental design consisted of three treatments per variety: a control versus traditional planktonic or biofilm inoculation, with three replicates per treatment. Germination at 10 days and seedling agronomical parameters showed that the response to seed inoculation was superior in the “Río Grande” variety. At harvest time, and irrespective of the inoculant, several agronomical parameters of the “Río Grande” variety were significantly enhanced with respect to the control. The biofilm significantly increased tomato production, as quantified by fruit number and weight, compared to the planktonic inoculum. This case study demonstrates that the incorporation of bio-inoculants is relevant in sustainable agriculture to promote crop growth and quality.