Cacao agroforestry system provides productive land use and preserves the best conditions for physical, chemical and biological properties of tropical soils in cocoa tropical region of the world. We evaluated the impact of changing a 30-year-old native secondary forest to two cacao agroforestry systems on soil fungal diversity. The cacao agroforestry systems adapted were: an improved natural agroforestry system (INAS) where trees without economic value were selectively removed to provide 50% shade; and an improved traditional agroforestry system (ITAS) where all native trees were cut and burnt in the location. In both systems, new economically valuable trees were planted. In these management systems, plots of 10 cacao genotypes and one plot with a spontaneous cacao hybrid were selected for soil sampling. In each plot, soil samples were randomly collected at 0–20 cm depth, immediately after the trees were planted (2004) and at the end of 2010; each sample was divided in two, one part for soil characterization by conventional chemical analytical methods and the other for soil fungal analysis using the plate dilution method. Soil fungi were identified by appropriate keys and grouped according to their functionality as potential biocontrol, plant pathogenic, facultative or saprophytic fungi; the structure of fungal communities was analyzed by population, richness and Shannon and Simpson indices. Fungal diversity varied significantly during the years of study, at all soil depths and under the agroforestry systems assessed. The fungal communities showed significant changes due to soil management influenced by INAS and ITAS, and mainly after burning of native vegetation in ITAS. Overall higher abundance of soil fungal communities were observed in ITAS than in INAS. In both systems, differential changes in soil physical and chemical properties under cacao also could have been a contributing factor in the fungal diversity and functional groups observed.