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The effect of organic manure on the community of mycorrhizal fungi (AMF) was evaluated in maize, cowpea and cotton intercropping systems in a semi-arid region of Brazil over two consecutive years. The experiment was conducted using a randomized block design with four replicates and six soil treatments: (M) goat manure incorporated in the soil before planting; (G) gliricidia prunings incorporated before planting;, (M+G) manure and gliricidia incorporated before planting; (GS) gliricidia applied on the soil surface 45 days after planting; (M+GS) manure incorporated before planting and gliricidia applied to the surface 45 days after planting; and (C) control treatment without incorporation. It was not possible to identify the best treatment for both years in terms of spore density, mycorrhizal colonization and glomalin content. However, there was a significant effect from the fertilization treatments when compared to the control in most treatments. In both years, M+GS favored glomalin and AMF sporulation in the cotton plots. In the second year, which had low rainfall, there was an increase in production of spores, glomalin, colonization and AMF species richness irrespective of soil incorporation and culture. Plots that were fertilized with manure presented greater AMF species richness regardless of the year and crop type.