In this study we assessed the effect of native and exotic selected AM fungal inocula on plant growth and nutrient uptake in a low input, 2 years Trifolium alexandrinum–Zea mays crop rotation. First, we evaluated the effects of four exotic AM fungal isolates on T. alexandrinum physiological traits in greenhouse. Second, the field performances of T. alexandrinum inoculated with the exotic AMF, both single and mixed, were compared with those obtained with a native inoculum, using a multivariate analysis approach. Finally, we tested the residual effect of AM fungal field inoculation on the growth and nutrient uptake of maize as following crop.