Soil health is directly related to sustainable development goals (SDGs) and can be affected by inadequate management practices. In this work, soil edaphic respiration and changes in microbial biomass promoted by cover crops in an integrated crop–livestock system (ICLS) were evaluated using soil health indicators with the respirometry method. The design was completely randomized in a 3 × 6 factorial arrangement, and multivariate principal components analysis (PCA) was performed according to MANOVA. Edaphic respiration was determined based on the respirometry technique. The results showed that edaphic soil respiration was significant in the nine evaluation periods, demonstrating the importance of grass cover in edaphic respiration arising from the biological activity of microorganisms, which is directly related to the amount of soil organic carbon. The cover crops increased soil organic matter and consequently microbial respiratory activity.