ABSTRACT Background: Clay extraction sites result from mining activities they present sterile, compacted and low-nutrient soils. They have been housing eucalypts crops for wood production. Their management, together with green manure inoculated with symbiont microorganisms, can increase the efficiency of nutrient uptake and reduce the need for chemical fertilization. The aim of the present study is to assess the growth and uptake of macronutrients by Eucalyptus grandis seedlings grown in substrate from clay extraction sites, based on intercropping system farming, with green manure inoculated with rhizobia and/or arbuscular mycorrhizal fungi (AMFs). The experiment followed a completely randomized design, with three repetitions, and the following treatments: cultivation of eucalypt (no intercropping) inoculated, or not, with AMFs; eucalypt intercropping system with Canavalia ensiformis Lam. or Canavalia brasiliensis Mart ex Benth., inoculated, or not, with AMF´s and/or rhizobia. Isolates of the symbiont microorganism were collected from spontaneous plants grown in clay extraction-site soils. Eucalypt seedlings and green manure were grown, together, in 6 L pots filled with substrate from clay extraction sites. Green manure shoot was cut 45 days after cultivation and eucalypt was harvested 60 days after it. Results: Inoculation with AMF´s+ rhizobia reduced the C:N ratio and increased N and P acquisition by C. ensiformis. Conclusions: Inoculation of native AMFs from the clay extraction site was effective in boosting the growth and nutrient acquisition of eucalypt plants grown in this substrate, in cultivation intercropped, or not, with C. ensiformis or C. brasiliensis. It also reduced visible symptoms of nutritional deficiency. Ca, Mg and K concentration in eucalypt plants was not changed by green manure cultivation or by inoculation with AMFs or rhizobia.