Abstract: A pot experiment was conducted to observe the effect of effective microorganisms (EM) on vesicular arbuscular mycorrhizal (VAM) colonization, nodulation and crop growth in Trifolium alexandrianum L., in soils amended with farmyard manure (FYM) and green manure (GM). EM significantly enhanced mycorrhizal colonization in 60-day old plants in both types of soil. EM failed to induce any remarkable change in nodulation at this growth stage while it exhibited an inhibitory effect on root and shoot biomass production. After 80 days growth, EM treated plants exhibited no significant variation in mycorrhizal colonization than non-treated plants. EM application caused a significant reduction in nodule number while increased the size and biomass of nodules in both types of soils. EM application supported root growth in FYM amended soil, however, shoot growth was adversely affected at this growth stage. In GM amended soil EM inhibited both the root and shoot growth. EM failed to induce any relationship between VAM colonization, nodulation and plant growth.