Nutrient Profiling Systems provide frameworks to assess the healthfulness of foods based on food composition and are intended as inputs into strategies to improve diets. Many Nutrient Profiling Systems are founded on a reductionist assumption that the healthfulness of foods is determined by the sum of their individual nutrients, with no consideration for the extent and purpose of processing and its health implications. A novel Nutrient Profiling System called Food Compass attempted to address existing gaps and provide a more holistic assessment of the healthfulness of foods. We propose that the chosen algorithm is not well justified and produces results that fail to discriminate for common shortfall nutrients, exaggerate the risks associated with animal-source foods, and underestimate the risks associated with ultra-processed foods. We caution against the use of Food Compass in its current form to inform consumer choices, policies, programs, industry reformulations, and investment decisions.