The use of Life cycle assessment (LCA) methods is rapidly expanding as a means of estimating the biodiversity impacts of organisations across complex value chains. However, these methods have limitations and substantial uncertainties, which are rarely communicated in the results of LCAs. Drawing upon the ecological and LCA literature on uncertainty and two worked examples of biodiversity footprinting, we outline where different types of uncertainty occur across multiple stages of the LCA process, from input data to the choice of biodiversity metric. Some uncertainties are epistemic, incorporating structural (e.g., the types of pressures included in models), parametric (e.g., uncertainty around conversion factors), and measurement uncertainty, as well as natural variability, stochasticity, and information gaps.