A key challenge for ecological science is to understand how biodiversity loss is changing ecosystem structure and function at scales relevant for policy1. Almost all biodiversity metrics are challenging to disaggregate into ecosystem functions, in particular animal-mediated functions such as pollination, seed and nutrient dispersal, and predation. Here, we adopt an ecosystem energetics approach2 as a physically meaningful method of translating animal species composition into a suite of ecosystem functions. We quantify historical changes to energy flows through mammal- and bird-mediated ecosystem functions across sub-Saharan Africa.