Ecosystems are open systems connected through spatial flows of energy, matter, and nutrients. Predicting and managing ecosystem interdependence requires a rigorous quantitative understanding of the drivers and vectors that connect ecosystems across spatio-temporal scales. Animals act as such vectors when they transport nutrients across landscapes in the form of excreta, egesta, and their own bodies. Here, we introduce a methodological roadmap that combines movement, foraging, and ecosystem ecology to study the effects of animal-vectored nutrient transport on meta-ecosystems. The meta-ecosystem concept—the notion that ecosystems are connected in space and time by flows of energy, matter, and organisms across boundaries—provides a theoretical framework on which to base our understanding of animal-vectored nutrient transport. However, partly due to its high level of abstraction, there are few empirical tests of meta-ecosystem theory, and while we may label animals as important mediators of ecosystem services, we lack predictive inference of their relative roles and impacts on diverse ecosystems. Recently developed technologies and methods—tracking devices, mechanistic movement models, diet reconstruction techniques and remote sensing—have the potential to facilitate the quantification of animal-vectored nutrient flows and increase the predictive power of meta-ecosystem theory. Understanding the mechanisms by which animals shape ecosystem dynamics may be important for ongoing conservation, rewilding, and restoration initiatives around the world, and for more accurate models of ecosystem nutrient budgets. We provide conceptual examples that show how our proposed integration of methodologies could help investigate ecosystem impacts of animal movement. We conclude by describing practical applications to understanding cross-ecosystem contributions of animals on the move.