Understanding the role of diet in shaping the ecology and evolution of species is a steadfast pursuit. Yet, resolving the relative importance of dietary sources in an organisms’ energy and growth budgets is particularly difficult within nutritional symbioses – such as those ubiquitous amongst shallow marine invertebrates (corals, bivalves, jellyfish, sponges) and their microbial symbionts. Increasingly, stable isotope approaches are employed to resolve diet – often as an alternative to exhaustive and potentially misleading examinations of ingestion (e.g. particle removal, substrate depletion, etc.). Here, I will share results from a novel application of Stable Isotope Bayesian Ellipses in R (SIBER) to symbiotic partnerships – from reef building corals, to giant clams. Heterotrophy – as evidenced by little overlap in host and symbiont isotopic niche areas correlates well with large polyp size (corals) and slower growth rates (clams) – whereas autotrophy is linked to an elevated conservation status. Other factors, such as seasonal variation in trophic plasticity, fatty acid and amino acid compound-specific isotope analysis, and how all of this can inform effective management and restoration action will be discussed.