The introduction of nitrogen fixing bacteria (NFB) and arbuscular mycorrhizal fungi (AMF) into the soil is an advisable agricultural practice for the crop, since it enhances nutrient and water uptake and tolerance to biotic and abiotic stresses. The aim of this work was to study plant nutrition, biological nitrogen fixation (BNF) and crop yield and quality, after inoculating seeds with NFBs ((Rhizobium leguminosarum, Burkholderia cenocepacia, Burkholderia vietnamiensis)) and/or AMFs (Rhizophagus irregularis, Claroideoglomus etunicatum, Claroideoglomus claroideum and Funneliformis mosseae) in a fava bean crop in two seasons. The composition of the nodule bacterial community was evaluated by the high-throughput sequencing analysis of bacterial 16 S rRNA genes. It was found that microbial inoculation accompanied by a 20% decrease in mineral fertilization had no significant effect on crop yield or the nutritional characteristics compared with a non-inoculated crop, except for an increase in the grain protein content in inoculated plants. None of the inoculation treatments increased biological nitrogen fixation over a non-inoculated level. The bacterial rRNA analysis demonstrated that the genus Rhizobium predominated in all nodules, both in inoculated and non-inoculated treatments, suggesting the previous presence of these bacteria in the soil. In our study, inoculation with Rhizobium leguminosarum was the most effective treatment for increasing protein content in seeds, while Burkholderia sp. was not able to colonise the plant nodules. Inoculation techniques used in fava beans can be considered an environmentally friendly alternative, reducing the input of fertilizers, while maintaining crop yield and quality, with the additional benefit of increasing the grain protein content. However, further research is required on the selection and detection of efficient rhizobial strains under local field conditions, above all those related to pH and soil type, in order to achieve superior nitrogen-fixing bacteria.