Metal(loid)s are toxic to animal life, human health and plants; therefore, their removal from polluted areas is imperative in order to minimize their impact on the ecosystems. The use of plant-amendment-microorganism synergy is a promising option, but not yet fully explored, to manage lands contaminated with metal(loid)s. However, molecular factors and mechanisms underlying this interaction are almost unknown. The aim of the present study was to evaluate the effects of amendments and bacteria, both alone and in combination, on Arabidopsis thaliana grown on arsenic and lead polluted soils. To accomplish this aim, a pot experiment was performed testing the effect of biochar and/or autochthonous metal(loid) resistant Bacillus isolates on physicochemical soil properties and on plant growth and metal(loid) uptake/intake. Furthermore, bioinformatics-assisted proteomics was used to understand common and specific mechanisms regulating plant growth and metal(loid) tolerance in tested conditions. Results showed that biochar and/or Bacillus induced significant and positive effects on soil properties, increasing pH, C-tot, N-tot and P-tot concentrations and decreasing nutrients (N-av and P-av), As and Pb availability. Plant growth was also enhanced by addition of biochar and/or bacterial inoculum, reaching the maximum when biochar and microorganism were combined. The deciphering of molecular mechanisms revealed that combination of biochar and bacterial inoculation mitigate Arabidopsis growth and defense tradeoff, and underline the great potential of plant-biochar-inoculum synergic application in more effective and large scale-up phytostabilizing systems.