Banana production in Australia is currently worth $600 million annually, but is constantly threatened by root pathogens, such as plant-parasitic nematodes and Fusarium wilt (Fusarium oxysporum f. sp. cubense). To reduce the impacts of soil borne diseases on banana production, farm management interventions are being designed to enhance organisms which suppress pathogens, while maintaining productivity. A holistic view of soil functions with an understanding of the ecological interactions is therefore required to develop productive, disease suppressive farming systems. Soil nitrogen and organic matter are two factors that have a large impact on soil organisms, and can be manipulated by farm management. Their impacts on biological processes were monitored in field trials in north Queensland using soil nematodes community structures and Community Level Physiological Profiling using MicroResp™. Nitrogen is applied to bananas to enhance vegetative plant growth and maintain production. However, high soil nitrogen inputs tended to increase bacterial domination in the soil environment and lead to an increase in root pathogens. Organic matter inputs provide carbon substrates for soil organisms. By increasing the diversity of organic matter inputs, through vegetative groundcovers, it was possible to increase soil biological diversity. Furthermore, vegetative groundcovers tended to increase the proportion of nematodes involved in organic matter recycling and reduce the proportion of plant-parasitic nematodes. The use of vegetative groundcovers also led to suppression of Fusarium wilt symptoms determined through soil bioassays. The results indicated that through the careful manipulation of nitrogen and organic matters inputs it was possible to engineer banana cropping system that suppress soil borne diseases and maintaining productivity.