Plants growing in acidic soils frequently develop beneficial interactions with stress adapted microorganisms. In an acidic soil with Mn toxicity, the arbuscular mycorrhizal fungi (AMF) associated to Ornithopus compressus were found to benefit plant growth. In wheat, increased growth and lower shoot Mn levels were promoted by the presence of extraradical mycelium (ERM) developed by these AMF, but the levels of other metals are not yet evaluated. In the present study, Al, Fe and Zn levels were quantified, by inductively coupled plasma mass spectrometry (ICP-MS), in shoots of wheat grown in acidic soil without and with the previous development of AMF associated to O. compressus. Additionally, soil was disturbed to understand the influence of disrupting ERM structure. Shoots of wheat grown in undisturbed soil (intact ERM) more than doubled in dry weight. Toxic Mn levels reduced c.a. 4-fold while the concentrations of Al, Fe and Zn decreased 2.3, 1.5 and 2.3-fold, respectively. Disruption of ERM structure inhibited the decrease in metal levels in 55% and 28% for Mn and Zn, respectively, while for Al and Fe no substantial variations were observed. Under Mn toxicity, the colonization of wheat by intact ERM of AMF associated to O. compressus appears to manage the uptake of Al, Fe and Zn, and positively influence plant growth, in acidic soil. Further studies will focus on the subcellular distributions of these metals in wheat shoots to assess preferential sites of accumulation or action.