Integrated crop–livestock systems are recognized for intensifying food production as long as adequate management of grazing, fertilization, and liming is practiced. There is still a lack of information about the effect of these factors on the soil microbiological community. This study evaluated the effects of grazing, liming, and different P and K fertilization strategies on the soil microbial community and its relationship with soil chemical properties. For this purpose, a field experiment was established in 2017 on a subtropical Acrisol. Treatments consisted of two production systems: (i) integrated crop-livestock system (with winter sheep grazing) and (ii) specialized system (ungrazed), combined with two periods of P and K fertilization: (i) conventional fertilization (at soybean planting) and (ii) system fertilization (in the Italian ryegrass pasture). The effect of liming (with and without) was also evaluated. Eighteen months after lime application, the soil was sampled in the 0–5 and10–15 cm soil layers to evaluate soil chemical properties (pH, exchangeable Al, Ca, and Mg, available P and K, cation (Ca+Mg+K) saturation, and Al saturation) and soil microbial community composition. In the surface soil layer, a negative impact of lime application was observed for Gram+ bacteria (−29 %) and actinomycetes (−21 %), consequently decreasing the total bacterial community (−26 %) and total microbial biomass (−27 %). This negative impact of liming on Gram+ bacteria and actinomycetes was negatively related to the increase in soil pH, exchangeable Ca and Mg concentrations, and positively related to Al saturation and available K. The combination of an integrated system or system fertilization with lime increased arbuscular mycorrhizal fungi community 3.0-fold compared to a specialized system or conventional fertilization in the subsurface soil layer. In addition, sheep grazing increased saprophytic fungi biomass by 50 % in the subsurface soil layer compared to the specialized system. These positive impacts on the soil fungal community were probably associated with increased plant residue input. Sheep grazing and the fertilization strategy did not affect soil chemical properties or the microbial community at the soil surface. Liming, system fertilization, and sheep grazing benefitted the soil fungal community, thus improving soil health in highly weathered agricultural soils.