Soil acidification is an important problem worldwide, with acid soil comprising more than 40% of the world’s total arable land. Aluminium (Al) is the third most abundant element in Earth’s crust but is not toxic to plants in pH-neutral and alkaline conditions. However, in acid soils, concentrations of soluble Al increase, becoming toxic to plant roots. In this study, for the first time, we used synchrotron-based K-edge X-ray absorption near-edge structure (XANES) at the SGM beamline of the Canadian Light Source for direct in situ analyses of Al speciation in root tissues of soybean (Glycine max), two buckwheat (Fagopyrum tataricum) genotypes, and three arabidopsis (Arabidopsis thaliana) genotypes grown in nutrient solution. First, we examined the suitability of the Al K-edge, obtaining spectra for the three plant species were compared to those of nine standard compounds. It was found that the spectra obtained from root tissues of soybean and the two buckwheat genotypes were similar to those of Al-malate, Al-citrate, and Al-pectin, indicating that sixfold coordinated Al exists in root tissues of these two plant species. For arabidopsis, a different spectra showed that both fourfold and sixfold coordinated Al exists in its root tissues. Thus, although useful for distinguishing between fourfold and sixfold coordinated Al, K-edge XANES did not appear to be suitable for separating Al binding to some common physiologically-relevant compounds within plant tissues (i.e. pectin and simple organic acids). Therefore, we next examined the Al L-edge, and although it was less sensitive, the L-edge spectra were more expressive thereby enabling differentiation between these various compounds. The method developed in the present study will be of value in understanding interactions between toxic Al and plant roots.