The present work was aimed at investigating the effects of a four strains consortium – Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, and Burkholderia ambifaria – on crops of Allium cepa L. and soil health. The bacterial consortium was inoculated on onion seeds of two different varieties; inoculated seeds and control ones (treated with autoclaved inoculum) were sown in open-field and followed until harvest. Plant growth development parameters, as well as soil chemical and molecular profiles (DNA extraction and 16S community sequencing on the Mi-Seq Illumina platform), were investigated. The results showed a positive influence of bacterial application on plant growth, with increased plant height (+ 18%), total chlorophylls (+ 42%), crop yields (+ 13 %) and bulbs dry matter (+ 3%) than the control. The differences between control and treated experimental conditions were also underlined in the bulb extracts in terms of total phenolic contents (+25%) and antioxidant activities (+20%). Soil fertility and microbial community structure and diversity were also positively affected by bacterial presence. At harvest, the soil with the presence of bacterial consortium showed increased total organic carbon, organic matter and available P and higher concentrations of nutrients than control. The ecological indexes calculated on molecular profiles showed that community diversity was positively affected by the bacterial treatment. The present work allowed to remark the effective use of plant growth-promoting bacteria as valid fertilization strategy to improve yield in productive landscapes, whilst safeguarding soil biodiversity.