<p>In Portugal, the Montado ecosystem, (or Dehesa in Spain), characterized by the presence of cork and holm oaks, possess soils typically low in fertility, generally acidic, and contain high concentrations of metalloid ions, such as aluminium (Al) and manganese (Mn). Soil acidity restricts agricultural production by around 70% in potentially arable lands worldwide, mainly due to the effects associated with the toxicity of these two ions on plant growth. In this work, a field assay was carried out in such acidic soil in the south of Portugal, to which different treatments were applied, consisting of amendments with limestone and cellulosic sludge. The aim was to isolate and evaluate rhizobial strains (symbiotic nitrogen fixing bacteria) from different legume species grown under these soil treatments. The study focused on the molecular characterization of these strains and the evaluation of their nitrogen fixing capacity, as well as other important characteristics, such as manganese and aluminium tolerance, and motility assessed as swimming tests. As result of this work, it was possible to select four rhizobial strains that were highly efficient in nitrogen fixation, showing a symbiotic effectiveness superior to 100%, a high or medium tolerance to Mn(II) and Al(III) (140–1200&#xa0;mg L ⁻¹) and with high or medium motility (swimming), as evaluated by in vitro tests. Overall, this work provides important results toward developing a rhizobial consortium for future use as an elite inoculant in pastures containing annual <i>Trifolium</i> species adapted to the acidic soils of cork and holm oak ecosystems.</p>