Consumers are shifting towards plant-based diets, driven by both environmental and health reasons. This has led to the development of new plant-based meat alternatives (PBMAs) that are marketed as being sustainable and good for health. However, it remains unclear whether these novel PBMAs to replace animal foods carry the same established nutritional benefits as traditional plant-based diets based on pulses, legumes and vegetables. We modelled a reference omnivore diet using NHANES 2017–2018 data and compared it to diets that substituted animal products in the reference diet with either traditional or novel plant-based foods to create flexitarian, vegetarian and vegan diets matched for calories and macronutrients. With the exception of the traditional vegan diet, all diets with traditional plant-based substitutes met daily requirements for calcium, potassium, magnesium, phosphorus, zinc, iron and Vitamin B12 and were lower in saturated fat, sodium and sugar than the reference diet. Diets based on novel plant-based substitutes were below daily requirements for calcium, potassium, magnesium, zinc and Vitamin B12 and exceeded the reference diet for saturated fat, sodium and sugar. Much of the recent focus has been on protein quality and quantity, but our case study highlights the risk of unintentionally increasing undesirable nutrients while reducing the overall nutrient density of the diet when less healthy plant-based substitutes are selected. Opportunities exist for PBMA producers to enhance the nutrient profile and diversify the format of future plant-based foods that are marketed as healthy, sustainable alternatives to animal-based products.