Cowpea (Vigna unguiculata) is a nutritious legume crop for both its grain and leaves and comprises an important component in both human and animal nutrition. In Brazil, the use of mulch, such as coconut fiber, and organic fertilizers to maximize cowpea production offers an alternative to conventional mineral fertilizer strategies. Farming practices affect the diversity and activity of soil microorganisms, including arbuscular mycorrhizal fungi (AMF), important plant growth promoters for legumes. Our objective was to determine the effect of mulching with coconut fiber and manure on AMF diversity in cowpea. Soil samples were collected from an Experimental Station in Petrolina, NE Brazil: one Caatinga (natural dry‐forest vegetation), one fallow, and one experimental site established in the fallow area and cultivated with cowpea receiving cattle manure and four doses (0, 12, 24, 48 t/ha) of coconut fiber. AMF species richness, abundance, and diversity were evaluated. Sixty‐four AMF species were recorded, with predominance of Glomeraceae and Acaulosporaceae. Highest species richness (47) was recovered from the Caatinga but AMF diversity was also high in the cultivated sites, demonstrating the importance of mycotrophic plants, such as cowpea, in crop production systems for the maintenance of AMF species richness. Although several species, such as Claroideoglomus etunicatum, Acaulospora scrobiculata, Glomus trufemii, and Paraglomus pernambucanum, revealed pronounced sporulation patterns, even high doses of coconut fiber did not affect AMF richness and diversity, compared to fallow. Consequently, cultivation of mycotrophic plants and use of organic manures are able to maintain high AMF species richness in tropical agroecosystems.