The natural carbon isotope ratio of a heterotrophic organism will match that of its food source, providing researchers with a basis to hypothesize about nutrient cycling. Measuring these ratios in complex microbial communities presents a number of challenges; standard bulk isotope techniques lack the resolution necessary to assign isotope signatures to different taxonomic units and single cell approaches have relatively low throughput. To address these challenges, a protein-based stable isotope fingerprinting method focused on mixed microbial communities was developed. In this method, the isotope signatures intrinsic to mass spectra are matched to their respective taxonomically resolved protein annotations. Following validation with mock communities, a case study on a symbiotic system was used to demonstrate the potential of this method.