Excess and limited trace metal contents in soils and plants can limit crop yields and pose a risk for the environment and human health. This mini-review reports on the emerging approach of combining X-ray absorption spectroscopy (XAS) with isotope analyses to improve the understanding of metal speciation and dynamics in soil-plant systems. In soils and their components, shifts in isotope compositions could be in some cases linked to changing metal speciation and thereby provide information on processes that control the phytoavailability of metals. In plants, the XAS-isotope approach has potential to improve the understanding of how complex interactions of metal speciation, redox processes, and membrane transport control metal uptake and translocation to edible plant parts. Yet, the XAS-isotope approach proves to be in a rather exploratory phase, and many research gaps remain. Such limitations can be overcome by methodological improvements and combining the approach with molecular biology and modelling approaches.