Advancing soil health lies at the intersection of belowground microbial processes and aboveground land management. However, linking microbial processes to land use is difficult. Understanding the response of soil microbes to management factors will provide agricultural producers and land managers with information regarding best management practices that not only improve soil health, but also maximize profitability. This study advances the understanding of microbial responses to land management by measuring microbial response to a) amendment application and tile drainage to remediate sodic soils, b) cover crop growth and tile drainage to ameliorate saline soils and c) tillage and fertilizer management factors on Bradyrhizobium japonicum, a symbiotic bacteria needed for biological N fixation in soybeans (Glycine max L.). Multiple time point measurements of soil microbial enzymes and functional gene copy numbers from three field experiments were used to determine microbial responses to land management. Key findings indicate that gypsum amendment applications, although effective at reducing sodicity, reduce soil enzyme activity levels in the short-term while tile drainage has no effect on microbial response to sodic soils. This work also demonstrates that the quantity of nitrifiers and denitrifiers can be used as either short–term or long–term indicators of soil health which reflect overall ecosystem health in sodic soils. In contrast to sodic soils, nitrifiers and denitrifiers are not useful indicators of soil health in saline soils as these microbial communities exhibit salinity induced community tolerance. Finally, tillage system and N availability have the greatest effect on B. japonicum numbers and activity in the soil. The lower amount of N obtained from biological N fixation in soybeans grown under no till systems reflects the reduced reliance on B. japonicum for plant N needs. Inoculated populations of B. japonicum are important for early season biological N fixation, but persistent and diverse populations of B. japonicum play an important role in late season N fixation in the lateral soybean root nodules. Overall, this work demonstrates that monitoring soil microbial activity can be useful for producers and land managers looking to improve soil health.