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 also almost unknown. The aim of the present study was to characterize Arabidopsis thaliana growth and response on arsenic and lead polluted soil. To accomplish this aim, a pot experiment was performed testing the effect of biochar and/or autochthonous metal(loid) resistant Bacillus isolate on physico-chemical soil properties and on plant growth and metal(loid) uptake/intake. Furthermore, bioinformatics-assisted proteomics approach 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 inoculum, reaching the maximum when biochar and bacteria 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.