Soil with excess Mn induces toxicity and impairs crop growth. However, with the development in the soil of an intact extraradical mycelia (ERM) from arbuscular mycorrhizal fungi (AMF) symbiotic to native Mn-tolerant plants, wheat growth is promoted due to a stronger AMF colonization and subsequent increased protection against Mn toxicity. To determine the biochemical mechanisms of protection induced by this native ERM under Mn toxicity, wheat grown in soil from previously developedLolium rigidum(LOL) orOrnithopus compressus(ORN), both strongly mycotrophic plants, was compared to wheat grown in soil from previously developedSilene gallica(SIL), a non-mycotrophic plant. Wheat grown after LOL or ORN had 60% higher dry weight, ca. two-fold lower Mn levels and almost double P contents. Mn in the shoots was preferentially translocated to the apoplast along with Mg and P. The activity of catalase increased; however, guaiacol peroxidase (GPX) and superoxide dismutase (SOD) showed lower activities. Wheat grown after ORN differed from that grown after LOL by displaying slightly higher Mn levels, higher root Mg and Ca levels and higher GPX and Mn-SOD activities. The AMF consortia established from these native plants can promote distinct biochemical mechanisms for protecting wheat against Mn toxicity.