In the Yaqui Valley, the use of organic fertilizers tends to reduce soil degradation in wheat production; however, biological impacts of this practice on soils are not evaluated yet. The aim of this experiment was to quantify the impact of a shift from conventional to organic wheat farming on reduction of the soil fungal degradation, by analyzing cultivable soil fungal population and diversity. The hypothesis was that the input of organic fertilizers to wheat farming leads to positive changes on soil physicochemical properties, which benefits soil fungal populations and decrease degradation. Three wheat commercial fields under 1) conventional synthetic fertilization (SF), 2) synthetic fertilization plus organic fertilization (SF+OF) and 3) only organic fertilization (OF) were selected. The study site under OF and SF+OF sites vs. SF showed higher organic matter content (1.5, 1.6 vs. 0.45%), fungal population (1.7x10(5), 9.1x10(4) vs. 1.6x10(4) CFU g(-1) dry soil) and diversity (12, 12 vs. 2). Based on phylogenetic analysis, 9, 11, and 2 fungal genera were isolated from the study site under organic, synthetic + organic, and synthetic fertilization, respectively. The metabolic diversity of obtained fungal strains showed that the indole production ranged from 0.5 to 65.4 mg mL(-1) where the higher fungal indole producer was Stachybotrys sp. TSM35. The higher phosphate solubilization (21%) was observed by the strain Talaromyces pinophilus TSO42, and the higher siderophore producer strain was Volutella ciliata TSM43, 33.9%. In addition, 60% of the strains showed potential health risks (alpha- or beta-hemolysis). Shift from conventional to organic wheat farming accomplished positive changes on soil physicochemical properties and cultivable soil fungal populations, in diversity and metabolic traits. Microbiologic quality control of organic fertilizers is needed to avoid microbial hazards in agronomic systems, caused by the introduction of potentially pathogenic strains.