The objective of this study was to examine the effects of arbuscular mycorrhizal fungi (AMF) and organic manure on the growth and element uptake of Trifolium repens and the soil chemical and biological characteristics in sterilized and natural soils. An increase in organic manure input reduced mycorrhizal colonization in the sterilized soil treatment. In comparison to the treatments in which AMF inoculation did not occur, AMF inoculation significantly promoted the biomass of shoots and roots in the sterilized soil at the 2.5 and 5% organic manure incorporation levels, whereas AMF had no effect on biomass in the natural soil. Regardless of soil type and whether AMF inoculation occurred, the N, P, K and Mg concentrations of the shoots and roots and the Cd concentration of the roots were increased by organic manure amendment. In comparison to the 2.5% organic manure amendment treatment, the addition of 5% organic manure to the sterilized soil decreased the N, P, K, Ca and Cd contents in the absence of AMF but had no negative effect on the N, P, K, Mg and Cd contents in the presence of AMF. The soil available P, pH, microbial biomass carbon, microbial biomass nitrogen, dissolved organic carbon, diethylenetriamine pentaacetic acid (DTPA)-extractable Cd and root Cd concentrations increased with increasing organic manure input. These results indicate that additive effects of AMF inoculation and organic manure on the growth and nutrient contents of Trifolium repens occurred in the Cd-contaminated sterilized soil but not in the natural soil, implying the limited function of nonnative AMF introduced into natural soils.