Protein is a central component of health and nutrition. The current animal protein production systems might not be able meet this growing demand for food and protein while also meeting climate change policy commitments. Therefore, alternative sources of protein must be considered. This study uniquely compares animal-based protein sources (milk, beef, sheep meat) to plant-based protein (wheat, barley, oats) across a suite of economic, environmental, and nutritional metrics. Economic performance is measured through the gross margin earned by the farmer, environmental performance through the farm-level CO2 emissions, and the nutritional performance through the gross protein yield and the protein yield corrected for digestibility using the Digestible Indispensable Amino Acid Score (DIAAS). Findings indicate that cereal crops perform better in terms of environmental and nutritional aspects but lag significantly behind the best economically performing livestock-based system, dairying. Moreover, dairy farms produce less gross protein than crop-specialized farms, but they produce a similar amount of available protein on a per hectare basis, i.e., protein that can be utilized by the body after digestion. The results do not allow for a definitive answer as to which protein source is the most holistically sustainable as the relative efficiency depends on the metric considered.