Background: Sustainable plant-, algal-, and fungal-based alternative foods are required to feed the growing human population. The quality of such alternative foods depends not only on the nutrient content, but also on the amino acid composition and protein digestibility. The assessment of protein digestibility is typically considered at the level of ingredients, but these are blended and processed to formulate palatable foods. Scope and approach: This review highlights the importance of nutritional quality in alternative foods by focusing on protein digestibility at the level of blends and formulated products. We consider the effects of processing on protein digestibility and the important role of the food matrix. Finally, we consider the colonic fermentation of undigested protein and the role of fiber in alternative foods. Key findings and conclusions: Few studies have investigated protein digestibility after the blending and processing of ingredients derived from alternative protein sources or compared protein digestibility between animal-based and alternative food products. We find that processing can increase or decrease the in vitro protein digestibility of alternative foods, or in some cases has no effect. The architecture of the food matrix after processing requires further investigation as a determinant of protein digestibility-related food quality. Furthermore, the mastication of food has a significant impact on its protein digestibility, but most in vitro models do not include this step. To promote the production of beneficial metabolites during colonic fermentation, undigested protein should be accompanied by dietary fiber, even if this partially compromises the digestibility of the protein.