Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope analysis, we estimated the proportional contributions of essential amino acids (AA_ESS) synthesized by gut microbes to five co-occurring desert rodents representing herbivorous, omnivorous, and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (Dipodomys spp.) routed a substantial proportion (~40–50%) of their AA_ESS from gut microbes, while higher trophic level omnivores (Peromyscus spp.) and insectivores (Onychomys arenicola) obtained most of their AA_ESS (~58%) from plant-based energy channels but still received ~20% of their AA_ESS from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals.