Soil compost application is a common soil management practice used by small farmers of Central-South Chile that produces positive effects on soil properties and also promotes presence and activity of arbuscular mycorrhizal fungi (AMF). This fungi form symbiosis with plant roots improving plant nutrition, as well as producing glomalin, a glycoprotein that has been associated with soil aggregation stability. Therefore, the aim of this study was to evaluate, in an Ultisol from Central-South Chile, the effect of different doses of compost on some soil characteristics at the end of the third year of a crop sequence including wheat (Triticum aestivum L.), bean (Phaseolus vulgaris L.), and grassland (Lolium multiflorum Lam. associated with Trifolium repens L.). Studied soil characteristics included chemical (pH, available-P, organic C), biological (C and N biomass, AMF spore number, root colonization percentage, mycelium length, and glomalin content), as well as physical parameters (water holding capacity [WHC], and water stable aggregates [WSA]). Results showed that, in general, compost application increased soil pH, mycorrizal roots, mycelium length, glomalin levels, and WSA. Significant relationships were found between C and N biomass, C biomass and WSA, C biomass and glomalin, WSA and WHC, among others. Results suggest that compost application to this type of soil is a feasible option as a fertilizer substitute, and a way to avoid soil erosion by small local farmers involved in organic agriculture.