Extensive agriculture faces the challenge of maintaining soil health while meeting global food demands. This research explores how different farming practices influence soil microbial communities and their ecological functions across the Argentinean Pampas. By comparing conventional and no-till systems, monoculture versus diversified crop rotations, and the effects of agrochemical use, we demonstrate that agricultural management significantly alters soil bacterial diversity, community structure, and biogeochemical processes. Sustainable practices, such as no-till with crop rotation, contribute to preserving microbial diversity and enhance soil functions, resembling natural ecosystems. In contrast, intensive monocultures reduce microbial heterogeneity and disrupt key soil processes. We also identify microbial indicators that respond to management intensity, offering potential tools for assessing soil health. Additionally, we found that glyphosate degradation and denitrification activity depends on both soil properties and farming history. These findings highlight the importance of adopting diversified, conservation-oriented practices to promote long-term soil sustainability. By integrating microbial ecology with agronomic research, this work provides a framework for designing agricultural systems that balance productivity with environmental sustainability.