Biological functions in soils are a product of the diverse group of microbial communities and these are limited by environmental and soil constraints. In the low-fertility Australian cropping soils, long-term sustainability of crop productivity in organic farming systems, with no modern agrochemical inputs, depends upon the optimal functioning of soil microbiota communities. Knowledge on the status of soil microbial communities and functions in Australian organic farming systems, in particular the broad-acre cropping systems, is very limited. Using a polyphasic approach incorporating a diverse array of DNA and traditional microbiological methods, we measured (i) the genetic and catabolic diversity of soil microflora, (ii) population level of key functional groups and (iii) levels of biological processes involved in N and P mineralization for soils from organic farms and neighbouring conventional farms from 10 sites distributed across southern Australian cropping region. The genetic diversity of soil bacteria and fungal communities under organic farming systems was significantly different to that under conventional farming systems but soil type also had a significant effect. Genetic richness of soil bacteria was generally higher in organic farm soils whereas the richness of soil fungi was variable. Soils from no-till systems exhibited greater richness of soil fungi. Community level physiological profiling of soil microbial communities showed significant effects of farming system, soil type and season. Soil type had a greater effect on microbial biomass and activity levels than the farming system. Populations and activity of nitrifying organisms were higher in the organic farm soils where as activity of phosphatases were lower in the organic farm soils in South Australia. Differences in the levels of soilborne pathogen inocula between organic and conventional farming soils varied with pathogen type, e.g. Rhizoctonia solani AG8 inoculum was lower where as the levels of Pythium spp. were higher in organic farm soils compared to conventional farm soils. Populations of Trichoderma group B species were generally lower in the organic farm soils compared to conventional no-till soils. Overall the results showed that an enhanced soil microbial community and biological processes, relative to conventional systems, may not be a definitive feature of all organic systems and it is necessary to provide adequate levels of C inputs to meet the energy demand by the microbial communities in order to maintain or improve biological activities relevant to nutrient mineralization and plant health.