Research conducted by the Yield Decline Joint Venture has shown that productivity of the current sugarcane farming system can be increased significantly by soil fumigation or breaking the current monoculture. Associated with these treatments have been decreases in the numbers of cane-specific pathogens and, in most cases, an increase in beneficial biota. It has been suggested that these changes to soil biota are responsible for at least part of the recorded increases in productivity, and that the responses are mediated via improved root health. This paper examines the effect of fumigation and break treatments on availability of essential nutrients in the soil, the relative changes in nutrient concentrations in the plant and total crop nutrient uptake. In the case of nitrogen, the increased demand associated with the growth responses has been at least partly met by treatments causing higher concentrations of mineral nitrogen in the soil solution. However, treatments have had little or no effect on the concentrations and availability of other nutrients (e.g. P, K and Si) in the soil, and increased plant uptake is attributed to an increased root surface area and a more thorough exploitation of the soil volume ie. a more functional root system. We propose that the ability to maintain or increase concentrations of nutrients like potassium and silicon in plant biomass may provide an index of root system functionality.