Arbuscular mycorrhizal fungi help to reduce the damage caused by erosion and maintain soil structure through the production of mycelium and adhering substances. This study evaluated the structural stability; estimated the diversity and density of mycorrhizal spores present in three systems of soil (eroded, forest and coffee plantations) in the rural area of Dagua, Valle del Cauca, Colombia. The systems evaluated were classified as farms with intensive or agroecological management. There were 25 morphospecies of mycorrhiza grouped in 13 genera, being Glomus and Entrophospora the most representative. The mean index values of mean weight (DPM) and geometric (DGM) diameters and diversity of mycorrhizal spores were statistically higher in farms with agroecological management than in farms with intensive management. The aggregate stability analysis revealed that eroded soils have significantly lower stability than forest and crop soils. A statistically significant correlation was found between diversity (r = 0.579) and spore density (r = 0.66) regarding DGM, and DPM with Shannon diversity (r = 0.54). Differences in practices, use and soil management affect mycorrhizal diversity found on farms and its effect such as particle aggregation agent generates remarkable changes in the stability and soil structure of evaluated areas. It is concluded, that agroecological management tends to favour both mycorrhizae and the structure of soils.