The measurement of a soil property reflects the capacity of soil to function at a particular time, whereas knowledge of a soil’s resilience assists in the development of systems or practices that promote a stable biological functional capability. Both human induced and environmental stimulus and stress events can alter the composition and activity of microorganisms. The degree of redundancy in the species present and the nature of soil physico-chemical environment is suggested to determine the degree of resilience in biological functions. In agricultural soils, the depletion of carbon rich microsites can affect the distribution, diversity and metabolic status of microbial communities and the overall biological resilience. We investigated the impact of 3-5 years of crop rotation, tillage, stubble retention on microbial activity, diversity and resilience in field experiments on Alfisol (2) and Vertosol (1) soils in South Australia and New South Wales, Australia. Crop rotation, stubble retention and tillage practices significantly influenced the catabolic diversity of microbial communities. Exposure of soils to repeat wet-dry cycles (stress) resulted in a decline in the amoA copy number and rate of nitrification compared to those not subjected to stress, with the highest decline occurred in the legume-wheat rotation. The response of biological functions to stresses differed between cropping systems with lower resilience in soils from a fallow-crop rotation than under continuous cropping. The decline in the biological resilience of soils under fallow-crop rotations could be attributed to the boom-bust cycles of C availability. Stubble retained no-till systems showed greater stability of microbial catabolic potential than stubble raked or incorporated systems and this effect varied with soil type. Additional of biochar material had a significant influence on long-term resilience but the effect varied with soil type. In conclusion, a better understanding of the resilience of the system is also useful to understand the role of changing environments and climates on ecosystem function.