AbstractDietary proteins derived from animal sources, although containing well‐balanced profiles of essential amino acids, have considerable environmental and adverse health effects associated with the intake of some animal protein‐based products. Consuming foods based on animal proteins carries a higher risk of developing non‐communicable diseases such as cancer, heart disease, non‐alcoholic fatty liver disease (NAFLD), and inflammatory bowel disease (IBD). Moreover, dietary protein consumption is increasing due to population growth, posing a supply challenge. There is, therefore, growing interest in discovering novel alternative protein sources. In this context, microalgae have been recognized as strategic crops that can provide a sustainable source of protein. Compared to conventional high‐protein crops, using microalgal biomass for protein production presents several advantages in food and feed in terms of productivity, sustainability, and nutritional value. Moreover, microalgae positively impact the environment by not exploiting land or causing water pollution. Many studies have revealed the potential of microalgae as an alternative protein source with the added value of positive effects on human health due to their anti‐inflammatory, antioxidant, and anti‐cancer properties. The main emphasis of this review is on the potential health‐promoting applications of microalgae‐based proteins, peptides, and bioactive substances for IBD and NAFLD.