Crop rotation and stubble management practices provide options to improve and better manage soil biological functions by modifying populations and activities of beneficial and plant pathogenic microorganisms with consequences to production and soil biological health. Plant type can affect the functional capacity of different groups of biota in the root microbiome. Stubble retention and tillage practices modify the physico-chemical properties of soil habitat thereby influencing biological processes. 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. Effects of management practices such as crop rotation, tillage, stubble retention on microbial composition, microbial activity and resilience were measured in field experiments on Alfisol (2) and Vertosol (1) soils in South Australia. More than 75% of a functional microarray experimental probes (from14677 probes) gave the required signal intensity with 7.2% of them showing significant differences between the different rotation crops. Wheat-canola had the highest between-crop difference (477 probes), followed by wheat-pasture (318 probes) and wheat-rye (135 probes). Non-cereal rotational crops substantially reduced populations of soilborne pathogenic fungi and modified the catabolic diversity of general microbial communities. Removal of stubble, tillage and fallowing had negative effect on stability of biological functions  whereas the addition of biochar material had a significant influence on long-term resilience but the effect varied with soil type. With the current focus on security of food to feed the growing global populations through sustainable agricultural production systems there is a need to develop innovative cropping systems that are both economically and environmentally sustainable.