Increasing attention has focused on the capacity of current global food systems to provide accessible, affordable, and sustainable food to a growing human population, particularly amid ongoing climate and environmental changes. Concerns about the dysfunction of the global food system have led to the development of several initiatives to estimate current and predict future global nutrient supplies based on various climate, production, and demand scenarios. Yet none adequately accounts for differences in nutrient bioavailability across food groups. As nutrient bioavailability varies substantially between plant-source foods (PSFs) and animal-source foods (ASFs), accounting for these differences has important implications for global nutrient supplies and the environmental costs associated with their production. In this perspective, we highlight the variability in estimated bioavailabity across PSFs and ASFs for 27 key nutrients and the limited accounting for bioavailability in major studies and nutrition recommendations. We conclude with a discussion of current best practices, highlighting avenues for future research to account for bioavailability and to more accurately evaluate and propose nutritionally adequate diets. This perspective suggests that, although existing data limitations should not preclude food systems researchers from accounting for bioavailability, a concerted effort is needed to develop more consistent and representative estimates of bioavailability across a variety of nutrients.