The objective of this work was to evaluate soil biomass and microbial activity and soybean yield under different limestone and gypsum doses and different cover crops. The experiment was carried out in the experimental area of ​​the Fundação de Apoio a Pesquisa Agropecuária de Chapadão, on a Dystrophic Red Latosol, using cultivar Desafio. The experiment consisted of a randomized blocks design, in a split-plot factorial scheme (3x4x3), with three replications. Plots consisted of three gypsum doses: control (without gypsum), recommended dose (2.3 Mg ha-1), and double dose (4.6 Mg ha-1). Subplots consisted of four limestone doses (2, 4, and 6 Mg ha-1) and the control (without limestone). Each block had three different cover crops: Brachiaria, Millet, and allow. The values obtained with the test revealed that brachiaria had better basal respiration in the absence of gypsum. Conversely, millet had better basal respiration in with the gypsum dose. Basal respiration, using brachiaria as cover crop, was higher at the dose of 2700 kg ha-1 of limestone. However, for the fallow and the millet, basal respiration was higher when using the highest limestone dose of 6000 kg ha-1. The variable microbial biomass showed differences between cover crops only in the absence of gypsum. Brachiaria and fallow presented the highest mean for microbial biomass. The use of millet as a cover crop together with gypsum doses increased the microbial biomass. The variables mass of 100 grains and grain yield had higher mean at the limestone dose of 6000 kg ha-1 .