Understanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remain problematic because current methods become unmanageable as network complexity increases. We developed a generalization of previous indirect estimation methods assuming a steady-state system (Hunt et al.,); the model estimates energy fluxes in a top-down manner assuming system equilibrium; each node's losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://cran.rproject.org/web/packages/fluxweb/index.html). We also present how the framework can merge with the allometric theory of ecology (Brown, Gillooly, Allen, Savage, & West,; to calculate fluxes based on easily obtainable organism-level data (i.e., body masses and species groups—e.g., plants, animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production. The primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g., predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state. Overall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.